R/methylationAnalysis_Step1.r
In VilainLab/methometR: methometR: Extracting methylation information from Optical Genome Maps
Defines functions
extracting_modifying_methLabels
contigextract
molMethylRefLoc
molMethylLoc
nickReference
molNickLoc
untaringdirectoy
modmolcmap
readingXmap
readingCmap
Documented in
contigextract
extracting_modifying_methLabels
modmolcmap
molMethylLoc
molMethylRefLoc
molNickLoc
nickReference
readingCmap
readingXmap
untaringdirectoy
#' Reads Bionano Cmap files
#'
#' @param cmap character. Path to Bionano cmap file.
#' @return Data Frame Contains the cmap file information.
#' @examples
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' @import utils
#' @export
readingCmap <- function(cmap){
#Reading contig, molecule or reference cmap
cmap_temp<-file(cmap, "r")
cmap_temp1<-readLines(cmap_temp, n = -1)
close(cmap_temp)
g1 <- grep("#h", cmap_temp1)
g2 <- grep("#f ",cmap_temp1)
##Extracting data
if (g1+1 == g2){
##reading the cmap file
dat <- gsub("#h ", "", cmap_temp1)
#dat4 <- textConnection(dat[g1:length(dat)])
dat4 <- textConnection(dat[g1])
r1 <- read.table(dat4, sep = "\t",header=FALSE)
#dat4 <- textConnection(dat[g1:length(dat)])
g3<-g1+2
dat5 <- textConnection(dat[g3:length(dat)])
r2 <- read.table(dat5, sep = "\t",header=FALSE)
close(dat5)
r8 <- data.frame(r2)
nam <- tryCatch(
names(r8) <- as.character(unlist(r1)),
warning = function(w) {
print(paste("File:", cmap, "is empty"))
return (NA)
},
error = function(e) {
print(paste("File:", cmap, "is empty"))
return (NA)
}
)
###Returning the dara
if (length(nam) == 0){
return(NA)
}
else{
names(r8) <- nam
return(r8)
}
}
return(r8)
}
#' Reads Bionano xmap files
#'
#' @param xmap character. Path to Bionano xmap file.
#' @return Data Frame Contains the xmap file information.
#' @examples
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' modxmap <- readingXmap(xmap)
#' @import utils
#' @export
readingXmap <- function(xmap) {
##Reading contig-molecule or reference-contig xmap
xmap = xmap
conXmap <- file(xmap, "r")
r10 <- readLines(conXmap, n = -1)
close(conXmap)
datfinal <- data.frame()
g1 <- grep("#h ", r10)
g2 <- grep("#f ", r10)
##Reading contig xmap
if (g1+1 == g2){
dat <- gsub("#h ", "", r10)
#dat4 <- textConnection(dat[g1:length(dat)])
dat4 <- textConnection(dat[g1])
r1 <- read.table(dat4, sep = "\t",header=FALSE)
#dat4 <- textConnection(dat[g1:length(dat)])
g3<-g1+2
dat5 <- textConnection(dat[g3:length(dat)])
r2 <- read.table(dat5, sep = "\t",header=FALSE)
#r8<-data.frame(r2)
nam <- tryCatch(
names(r2) <- as.character(unlist(r1)),
warning = function(w) {
print(paste("File:", xmap, "is empty"))
return (NA)
},
error = function(e) {
print(paste("File:", xmap, "is empty"))
return (NA)
}
)
##Returning the data
if (length(nam) == 0){
return(NA)
}
else{
names(r2) <- nam
return(r2)
}
}
return(r2)
}
#' Identifies and documents the methylation and nick labels
#'
#' @param molcmap character. Path to Bionano molecule cmap.
#' @param xmapdata character. Path to Bionano molecule contig xmap.
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @return Data Frame with the molecule cmap, with the exact site number
#' for methylation and nick labels.
#' @examples
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' modxmap <- readingXmap(xmap)
#' modMolcmap <- modmolcmap(molcmap = modcmap,
#' xmapdata = modxmap,
#' cntNick = 1,
#' cntMeth=2)
#' @import utils
#' @export
modmolcmap <- function(molcmap, xmapdata, cntNick , cntMeth ){
print("Adding the label location to molecule files")
molCmapID <- as.numeric(unique(molcmap$CMapId))
dataContig<-data.frame()
datf<-data.frame()
datFinalmol <- data.frame()
xmapdata = xmapdata
molcmap = molcmap
cntNick = cntNick
cntMeth = cntMeth
###counting nick and methylation region in the molcmap
for (j in seq_along(molCmapID)){
#print(molCmapID[j])
dat3<-molcmap[which(molcmap$CMapId==molCmapID[j] &
(molcmap$LabelChannel == cntNick
| molcmap$LabelChannel == cntMeth)),]
datnick <- dat3[which(dat3$LabelChannel == cntNick),]
datmeth <- dat3[which(dat3$LabelChannel == cntMeth),]
orientMol <- c()
countnick <- c()
countmeth <- c()
molxmap <- xmapdata[which(xmapdata$QryContigID == molCmapID[j]),]
dat4 <- molcmap[which(molcmap$CMapId==molCmapID[j]
& molcmap$LabelChannel == 0),]
dat4 <- cbind(dat4[,1:4],
NickLoc = "-",
MethLoc = "-",
OrientationMolecule = molxmap$Orientation,
dat4[,5:ncol(dat4)],
row.names = NULL)
cntnickneg = nrow(datnick) + 1; cntmethneg = nrow(datmeth) + 1
orient <- unique(as.character(molxmap$Orientation))
cntnickpos = 0; cntmethpos = 0
for (hh in 1:nrow(dat3)){
if(as.numeric(dat3$LabelChannel[hh])== cntNick){
cntnickpos = cntnickpos + 1
#print(paste("hh:", hh, "cntnickpos:", cntnickpos))
countnick<-c(countnick,cntnickpos)
orientMol <- c(orientMol, orient)
countmeth<-c(countmeth,0)
}
else if(as.numeric(dat3$LabelChannel[hh])== cntMeth){
cntmethpos = cntmethpos + 1
countmeth<-c(countmeth,cntmethpos)
orientMol <- c(orientMol, orient)
countnick<-c(countnick,0)
}
else {
countmeth<-c(countmeth,0)
countnick<-c(countnick,0)
}
}
datt<-cbind(dat3[,1:4],
NickLoc = countnick,
MethLoc = countmeth,
OrientationMolecule = orientMol,
dat3[,5:ncol(dat3)],
row.names = NULL)
datt <- rbind(datt, dat4,row.names = NULL)
datf<-rbind(datf,datt,row.names = NULL)
}
'qrycmapData <- cmap
qrycontig <- as.numeric(unique(cmap$CMapId))
datf<-data.frame()
for (j in 1:length(qrycontig)){
dat3<-qrycmapData[which(qrycmapData$CMapId == qrycontig[j]),]
cntnick=0;cntmeth=0;countnick<-c();countmeth<-c()
for (hh in 1:nrow(dat3)){
if(as.numeric(dat3$LabelChannel[hh])==2){
cntnick=cntnick+1
countnick<-c(countnick,cntnick)
countmeth<-c(countmeth,0)
}else if(as.numeric(dat3$LabelChannel[hh])==1){
cntmeth=cntmeth+1
countmeth<-c(countmeth,cntmeth)
countnick<-c(countnick,0)
}else {
countmeth<-c(countmeth,0)
countnick<-c(countnick,0)
}
}
datt<-cbind(dat3[,1:4],NickLoc=countnick,MethLoc=countmeth,dat3[,5:ncol(dat3)])
datf<-rbind(datf,datt)
}'
return (datf)
}
#' Untarring the directory if needed
#'
#' @param cmaploc_mol character. Path to Bionano compressed file.
#' @return uncompressed folder with all the files for analysis
#' @examples
#' cmaploc_mol <- system.file("extdata", package="methometR")
#' untarredFolder <-untaringdirectoy(cmaploc_mol)
#' @importFrom utils untar
#' @export
untaringdirectoy <- function(cmaploc_mol){
print("Untaring directories if untarring option chosen")
untar(file.path(cmaploc_mol,"molecules.tar.gz"), exdir = cmaploc_mol)
lmolecules <- list.files(paste0(cmaploc_mol, "molecules/output/contigs/exp_refineFinal1/merged_smaps"), pattern = "*_q.cmap", full.names = TRUE)
return(lmolecules)
}
#' Mapping nick label location from contig to molecule
#'
#' @param nickrefLoc character. contig cmap data.
#' @param molcmap character. molecule cmap data.
#' @param xmapdata character. contig-molecule xmap data.
#' @param contigID character. query contig ID.
#' @param nickrefLoc character. Path to Bionano compressed file.
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @return dataframe containing the molecule file, with the nick position
#' @examples
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
#' Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
#' refxmapdat <- readingXmap(refcontigXmap)
#' refcmapdat <- readingCmap(refCmap)
#' contigcmapdat <- readingCmap(Contigqcmap)
#' nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat,
#' contigcmap = contigcmapdat, contigID = 6701,
#' returnMethod =c("dataFrame"), chrom = 4)
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' molcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' contigcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContig_r.cmap", package="methometR")
#' contigID = 6701; cntNick = 1; cntMeth=2
#' modxmap <- readingXmap(xmap)
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' modMolcmap <- modmolcmap(molcmap = modcmap,
#' xmapdata = modxmap,
#' cntNick = 1,
#' cntMeth=2)
#' contigmodcmap <- readingXmap(contigcmap)
#' modmolcmapNick <-molNickLoc(nickrefLoc = nickRef,
#' molcmap = modMolcmap,
#' xmapdata = modxmap,
#' contigID = contigID, cntNick = cntNick,
#' cntMeth = cntMeth)
#' @import utils
#' @export
molNickLoc <- function(nickrefLoc,molcmap,xmapdata, contigID, cntNick ,
cntMeth){
print("Searching for the nick labels in the molecules")
'cl <- makeCluster(5) #not to overload your computer
print(cl)
registerDoParallel(cl)'
molcmap <- molcmap
datf <- molcmap
xmapdata <- xmapdata
datFinal <- nickrefLoc
contigID = contigID
cntNick = cntNick
cntMeth = cntMeth
'print(paste("CntNick: ", cntNick))
print(paste("cntMeth: ", cntMeth))'
datFinalmol <- data.frame()
###Identifying the molecule ID
#molCmapID<-as.numeric(unique(molcmap$CMapId))
molCmapID<-as.numeric(unique(molcmap$CMapId))
#datFinalmol <- foreach (ui = 1:length(molCmapID), .combine=rbind) %dopar% {
###Extracting the site IDs of the query(moleule) and reference(contig)
for(ui in 1:length(molCmapID)){
#print(ui)
#print(paste("CmapID",molCmapID[ui]))
refloc2<-c();queryloc2<-c()
#qrycontig<-as.numeric(dat1$QryContigID)
dattt<-xmapdata[which(as.numeric(xmapdata$QryContigID) == molCmapID[ui]),]
alnt<-dattt$Alignment
refloc3<-c();queryloc2<-c()
if(length(alnt) > 1){
for(ii in length(alnt)){
stt<-strsplit(as.character(alnt[ii]),split="\\)\\(")
stt1<-as.character(stt[[1]])
for (ti in 1:length(stt1)){
if(length(grep("\\(",stt1[ti]))==1){
st2<-strsplit(stt1[ti],split="\\(")
st3<-strsplit(st2[[1]][2],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
else if(length(grep("\\)",stt1[ti]))==1){
st2<-strsplit(stt1[ti],split="\\)")
st3<-strsplit(st2[[1]][1],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
else{
st3<-strsplit(stt1[ti],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
}
}
}else{
stt<-strsplit(as.character(alnt),split="\\)\\(")
stt1<-as.character(stt[[1]])
for (ti in 1:length(stt1)){
if(length(grep("\\(",stt1[ti]))==1){
st2<-strsplit(stt1[ti],split="\\(")
st3<-strsplit(st2[[1]][2],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
else if(length(grep("\\)",stt1[ti]))==1){
st2<-strsplit(stt1[ti],split="\\)")
st3<-strsplit(st2[[1]][1],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
else{
st3<-strsplit(stt1[ti],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
}
}
dattempcont <- data.frame(QueryID = queryloc2, RefID = refloc3)
###Extracting based on the refl
LocRef<-c();chrompos<-c();chromosome<-c();contigsiteID <- c()
molsiteID <- c(); contig <- c()
'datttt <- datf[which(datf$CMapId == molCmapID[ui] &
datf$LabelChannel == cntNick),]
queryloc3 <- datttt$NickLoc
unqueryloc <- unique(queryloc3)'
unqueryloc <- unique(queryloc2)
for (ll in 1:length(unqueryloc)){
#k1<-as.numeric(hash::keys(h))
#print(as.numeric(refloc2[ll]))
#val1<-as.numeric(hash::values(h,keys=as.numeric(refloc2[ll])))
datp <- dattempcont[which(dattempcont$QueryID == unqueryloc[ll]),]
val <- c()
val <- datp$RefID
#print(val)
if(length(val)> 1){
for( ql in 1:length(val)){
#val <- hash::values(ha6, keys = queryloc3[ll])
dattem<-datFinal[which(as.numeric(datFinal$CMapId) == contigID
& as.numeric(datFinal$SiteID) == val[ql]),]
#print(dim(dattem))
if(nrow(dattem) >= 1){
for(yu in 1:nrow(dattem)){
#print(paste("CMapID",cmapID[ii],sep=""))
LocRef<-c(LocRef,as.numeric(dattem$Position[yu]))
chrompos <- c(chrompos,as.numeric(dattem$chromosomePosition[yu]))
contig <- c(contig, contigID)
contigsiteID <- c(contigsiteID, dattem$SiteID[yu])
molsiteID <- c(molsiteID, unqueryloc[ll])
chromosome<-c(chromosome,as.numeric(dattem$chromosome[yu]))
}
}else{
#print(paste("CMapID",cmapID[ii],sep=""))
LocRef<-c(LocRef,0)
chrompos <- c(chrompos,NA)
contig <- c(contig, contigID)
contigsiteID <- c(contigsiteID, 0)
molsiteID <- c(molsiteID, unqueryloc[ll])
chromosome<-c(chromosome,as.numeric(dattem$chromosome[yu]))
}
}
}else{
#val <- hash::values(ha6, keys = queryloc3[ll])
dattem<-datFinal[which(as.numeric(datFinal$CMapId) == contigID
& as.numeric(datFinal$SiteID) == val),]
#print(dim(dattem))
if(nrow(dattem) >= 1){
for(yu in 1:nrow(dattem)){
#print(paste("CMapID",cmapID[ii],sep=""))
LocRef<-c(LocRef,as.numeric(dattem$Position[yu]))
chrompos <- c(chrompos,as.numeric(dattem$chromosomePosition[yu]))
contig <- c(contig, contigID)
contigsiteID <- c(contigsiteID, dattem$SiteID[yu])
molsiteID <- c(molsiteID, unqueryloc[ll])
chromosome<-c(chromosome,as.numeric(dattem$chromosome[yu]))
}
}else{
#print(paste("CMapID",cmapID[ii],sep=""))
LocRef<-c(LocRef,0)
chrompos <- c(chrompos,NA)
contig <- c(contig, contigID)
contigsiteID <- c(contigsiteID, 0)
molsiteID <- c(molsiteID, unqueryloc[ll])
chromosome<-c(chromosome,chromosome,as.numeric(dattem$chromosome[yu]))
}
}
}
datmol<-data.frame(
cmapid = rep(as.character(molCmapID[ui]),length(LocRef)),
chromosome = chromosome,
chrompos = chrompos,
LocRef=LocRef,
ContigID = contig,
ContigSiteID = contigsiteID,
MolsiteID = molsiteID)
cmapID<-unique(datmol$cmapid)
#print(cmapID)
dattemp1<-datmol[which((datmol$cmapid) == cmapID),]
datftemp<-datf[which(as.numeric(datf$CMapId) == cmapID),]
chromo = unique(datmol$chromosome)
'contigSiteID <- as.numeric(dattemp1$ContigSiteID)
Position <- (as.numeric(dattemp1$LocRef))'
molsiteID <- as.numeric(unique(dattemp1$MolsiteID))
ik = 1; ij = 0
OrientationMolecule <- as.character(unique(datftemp$OrientationMolecule))
#pnc <- paste("^", datftemp$NickLoc, "$", sep ="")
if(OrientationMolecule == "-"){
len <- nrow(datftemp)
datFinalmol_rep <- data.frame()
for(qi in nrow(datftemp):1){
#print(qi)
if(datftemp$LabelChannel[qi] == cntNick){
#dattemp3 <- datftemp[which(as.numeric((datftemp$NickLoc)[qi]) == molsiteID[ik]),]
#print(paste("molsiteID[ik]:",molsiteID[ik]))
#print(paste("ik",ik))
if(is.na(molsiteID[ik])) {
molsiteID[ik] = 0
} else{
molsiteID[ik] = molsiteID[ik]
}
if(datftemp$NickLoc[qi] == as.character(molsiteID[ik])){
dattemp2 <- dattemp1[which((dattemp1$MolsiteID) == molsiteID[ik]),]
#print(names(dattemp2))
contigSiteID <- as.numeric(dattemp2$ContigSiteID)
Position <- (as.numeric(dattemp2$LocRef))
Contig <- dattemp2$ContigID
#print(Contig)
chromPosition <- as.numeric(dattemp2$chrompos)
chromosome <- as.numeric(dattemp2$chromosome)
if(length(contigSiteID)> 1){
'print(qi)
print(OrientationMolecule)'
for(lo in 1:length(contigSiteID)){
datt<-cbind(datftemp[qi,1:4],
chromosome = chromosome[lo],
chromPosition = chromPosition[lo],
contigPosition = Position[lo],
ContigID = Contig[lo],
contigSiteID = contigSiteID[lo],
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
}
}else{
datt<-cbind(datftemp[qi,1:4],
chromosome = chromosome,
chromPosition = chromPosition,
contigPosition = Position,
ContigID = Contig,
contigSiteID = contigSiteID,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
}
ik = ik+1
}else{
#chromosome <- as.numeric(unique(dattemp2$chromosome))
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
next
}
}else if(datftemp$LabelChannel[qi] == cntMeth){
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
}else{
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
}
}
datFinalmol_rep1 <-datFinalmol_rep[order(datFinalmol_rep$SiteID),]
datFinalmol <- rbind(datFinalmol, datFinalmol_rep1,row.names = NULL)
} else if(OrientationMolecule == "+"){
for(qi in 1:nrow(datftemp)){
#print(qi)
if(datftemp$LabelChannel[qi] == cntNick){
#dattemp3 <- datftemp[which(as.numeric((datftemp$NickLoc)[qi]) == molsiteID[ik]),]
#print(paste("molsiteID[ik]:",molsiteID[ik]))
#print(paste("ik",ik))
if(is.na(molsiteID[ik])) {
molsiteID[ik] = 0
} else{
molsiteID[ik] = molsiteID[ik]
}
if(datftemp$NickLoc[qi] == as.character(molsiteID[ik])){
dattemp2 <- dattemp1[which((dattemp1$MolsiteID) == molsiteID[ik]),]
#print(names(dattemp2))
contigSiteID <- as.numeric(dattemp2$ContigSiteID)
Position <- (as.numeric(dattemp2$LocRef))
Contig <- dattemp2$ContigID
#print(Contig)
chromPosition <- as.numeric(dattemp2$chrompos)
chromosome <- as.numeric(dattemp2$chromosome)
if(length(contigSiteID)> 1){
'print(1)
print(qi)
print(OrientationMolecule)'
for(lo in 1:length(contigSiteID)){
datt<-cbind(datftemp[qi,1:4],
chromosome = chromosome[lo],
chromPosition = chromPosition[lo],
contigPosition = Position[lo],
ContigID = Contig[lo],
contigSiteID = contigSiteID[lo],
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
}
}else{
'print(2)
print(qi)
print(OrientationMolecule)'
datt<-cbind(datftemp[qi,1:4],
chromosome = chromosome,
chromPosition = chromPosition,
contigPosition = Position,
ContigID = Contig,
contigSiteID = contigSiteID,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
}
ik = ik+1
}else{
'print(3)
print(qi)
print(OrientationMolecule)'
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)])
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
next
}
}else if(datftemp$LabelChannel[qi] == cntMeth){
'print(4)
print(qi)
print(OrientationMolecule)'
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)])
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
}else{
'print(5)
print(qi)
print(OrientationMolecule)'
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)])
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
}
}
}else{
print("Orientation not present")
}
}
#stopImplicitCluster(cl)
return(datFinalmol)
}
#' Mapping nick label location from contig to reference
#'
#' @param refxmap character. contig reference xmap data.
#' @param refcmap character. reference cmap data.
#' @param contigcmap character. contig cmap data.
#' @param contigID character. query contig ID.
#' @param returnMethod character. Output method. Text or dataframe.
#' @param hmdir integer. Home Directory.
#' @param chrom integer. chromosome number.
#' @return dataframe containing the molecule file, with the reference position
#' @examples
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
#' Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
#' refxmapdat <- readingXmap(refcontigXmap)
#' refcmapdat <- readingCmap(refCmap)
#' contigcmapdat <- readingCmap(Contigqcmap)
#' nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat,
#' contigcmap = contigcmapdat, contigID = 6701,
#' returnMethod =c("dataFrame"), chrom = 4)
#' @import utils
#' @import data.table
#' @export
nickReference <- function(refxmap, refcmap, contigcmap, contigID,
returnMethod =c("Text", "dataFrame"), hmdir, chrom){
print("Searching for the nick labels in the reference")
refxmap = refxmap
contigcmap <- contigcmap
contigID = contigID
chrom = chrom[1]
#print(contigID)
#print(contigID)
dat1 <- refxmap[which(refxmap$QryContigID == contigID
& refxmap$RefContigID == chrom),]
aln<-dat1$Alignment
if(length(aln) > 1){
dat <- data.frame()
for(z in 1:length(aln)){
st<-strsplit(as.character(aln[z]),split="\\)\\(")
#st1<-as.character(st[[1]])
datt <- data.frame()
for(i in 1:length(st)){
st1 <- st[[i]]
queryloc<-c(); refloc <- c()
for (ti in 1:length(st1)){
if(length(grep("\\(",st1[ti]))==1){
st2<-strsplit(st1[ti],split="\\(")
st3<-strsplit(st2[[1]][2],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
else if(length(grep("\\)",st1[ti]))==1){
st2<-strsplit(st1[ti],split="\\)")
st3<-strsplit(st2[[1]][1],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
else{
st3<-strsplit(st1[ti],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
}
queryLoc = as.numeric(queryloc)
h<-data.table(queryLoc = as.numeric(queryloc),
refLoc = as.numeric(refloc))
setkey(h, queryLoc)
#.set(h, keys=as.numeric(queryloc),values=as.numeric(refloc))
###Getting unique cmapID
contCmapID <- as.numeric(unique(dat1$QryContigID)[i])
#datFinal <- data.frame()
datFinalmol <- data.frame()
LocRef<-c();cmapid<-c();chromosome<-c(); queryref <- c(); siteID <- c()
k1 <- as.numeric(unique(queryLoc))
for (ll in 1:length(queryloc)){
if(length(grep(paste("^",as.numeric(queryloc[ll]),"$",sep=""),k1))>=1){
#print(as.numeric(queryloc[ll]))
#val1<-as.numeric(hash::values(h,keys=as.numeric(queryloc[ll])))
val1 <- h[.(as.numeric(k1[ll]))]
ref <- val1$refLoc
dattem<-refcmap[which(as.numeric(refcmap$CMapId)==chrom
& as.numeric(refcmap$SiteID) %in% ref),]
#print(dim(dattem))
LocRef<-c(LocRef,as.numeric(dattem$Position))
cmapid<-c(cmapid,as.numeric(contCmapID))
chromosome<-c(chromosome,chrom)
queryref <- c(queryref, as.numeric(queryloc[ll]))
}else{
#print(paste("CMapID",CmapID[ui],sep=""))
LocRef<-c(LocRef,0)
cmapid<-c(cmapid,as.numeric(contCmapID))
chromosome<-c(chromosome,chrom)
queryref <- c(queryref, as.numeric(queryloc[ll]))
}
}
dattemp<-data.frame(Chromosome=chromosome,cmapid=cmapid,LocRef=LocRef, queryref = queryref)
#write.table(dattemp, paste0("Contig_", unique(cmapid), "_r_mod.cmap"), row.names = FALSE)
datt <- rbind(datt, dattemp,row.names = NULL)
}
dat <- rbind(dat,datt,row.names = NULL)
}
}else{
st<-strsplit(as.character(aln),split="\\)\\(")
#st1<-as.character(st[[1]])
dat <- data.frame()
for(i in 1:length(st)){
st1 <- st[[i]]
queryloc<-c(); refloc <- c()
for (ti in 1:length(st1)){
if(length(grep("\\(",st1[ti]))==1){
st2<-strsplit(st1[ti],split="\\(")
st3<-strsplit(st2[[1]][2],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
else if(length(grep("\\)",st1[ti]))==1){
st2<-strsplit(st1[ti],split="\\)")
st3<-strsplit(st2[[1]][1],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
else{
st3<-strsplit(st1[ti],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
}
'h<-hash()
.set(h, keys=as.numeric(queryloc),values=as.numeric(refloc))'
queryLoc = as.numeric(queryloc)
h<-data.table(queryLoc = as.numeric(queryloc),
refLoc = as.numeric(refloc))
setkey(h, queryLoc)
###Getting unique cmapID
contCmapID <- as.numeric(unique(dat1$QryContigID)[i])
#datFinal <- data.frame()
datFinalmol <- data.frame()
LocRef<-c();cmapid<-c();chromosome<-c(); queryref <- c(); siteID <- c()
#k1<-as.numeric(hash::keys(h))
k1 <- as.numeric(unique(h$queryLoc))
for (ll in 1:length(queryloc)){
if(length(grep(paste("^",as.numeric(queryloc[ll]),"$",sep=""),k1))>=1){
#print(as.numeric(queryloc[ll]))
val1 <- h[.(as.numeric(k1[ll]))]
ref <- val1$refLoc
dattem<-refcmap[which(as.numeric(refcmap$CMapId)==chrom
& as.numeric(refcmap$SiteID) %in% ref),]
#print(dim(dattem))
LocRef<-c(LocRef,as.numeric(dattem$Position))
cmapid<-c(cmapid,as.numeric(contCmapID))
chromosome<-c(chromosome,chrom)
queryref <- c(queryref, as.numeric(queryloc[ll]))
}else{
#print(paste("CMapID",CmapID[ui],sep=""))
LocRef<-c(LocRef,0)
cmapid<-c(cmapid,as.numeric(contCmapID))
chromosome<-c(chromosome,chrom)
queryref <- c(queryref, as.numeric(queryloc[ll]))
}
}
dattemp<-data.frame(Chromosome=chromosome,cmapid=cmapid,LocRef=LocRef, queryref = queryref)
#write.table(dattemp, paste0("Contig_", unique(cmapid), "_r_mod.cmap"), row.names = FALSE)
dat <- rbind(dat, dattemp,row.names = NULL)
}
}
####Methylation generation
cmapID<-as.numeric(unique(dat$cmapid))
datFinal <- data.frame()
#dattemp1<-dat[which(as.numeric(dat$cmapid)==cmapID),]
if(length(cmapID) > 1){
for(oo in 1:length(cmapID)){
#print(oo)
datftemp <- contigcmap[which(as.numeric(contigcmap$CMapId) == cmapID[oo]),]
#chromosome=dattemp1$Chromosome
datc <- dat[which(dat$cmapid ==cmapID[oo]),]
Position=(as.numeric(datc$LocRef))
qry <- (as.numeric(datc$queryref))
pqry <- paste0("^", qry , "$")
for( yy in 1:nrow(datftemp)){
if(as.numeric(datftemp$LabelChannel[yy])==1){
passite <- paste0("^", datftemp$SiteID[yy], "$")
g1 <- grep(passite, pqry, fixed = TRUE)
if(length(g1) == 1){
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = Position[g1],
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
else if(length(g1) > 1){
dattt <- data.frame()
for (nn in 1:length(g1)){
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = Position[g1[nn]],
datftemp[yy,7:ncol(datftemp)])
dattt <- rbind(dattt, datt, row.names = NULL)
}
datFinal<-rbind(datFinal,dattt, row.names = NULL)
}else {
'print(paste0("Locations dont match :",
datftemp$SiteID[yy]))'
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = NA,
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
}
else if(as.numeric(datftemp$LabelChannel[yy]) == 0){
posn <- Position[yy-1]
pos <- posn + (datftemp$Position[yy]-datftemp$Position[yy-1])
datt<-cbind(datftemp[yy,1:6],
chromosome=chrom,
chromosomePosition=pos,
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
else{
print("Inappropriate label")
}
}
'write.table(datFinal, file.path(hmdir, paste0("Contigs_",
cmapID[oo], "_q.cmap")),
sep = "\t",row.names = FALSE)'
}
} else if (length(cmapID) == 1){
datftemp <- contigcmap[which(as.numeric(contigcmap$CMapId)==cmapID),]
#chromosome=dattemp1$Chromosome
datc <- dat[which(dat$cmapid ==cmapID),]
Position=(as.numeric(datc$LocRef))
qry <- (as.numeric(datc$queryref))
pqry <- paste0("^", qry , "$")
for( yy in 1:nrow(datftemp)){
'print(cmapID)
print(yy)'
if(as.numeric(datftemp$LabelChannel[yy])==1){
passite <- paste0("^", datftemp$SiteID[yy], "$")
g1 <- grep(passite, pqry, fixed = TRUE)
if(length(g1) == 1){
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = Position[g1],
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
else if(length(g1) > 1){
for(pp in 1:length(g1)){
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = Position[g1[pp]],
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
}else {
#print(paste0("Locations don't match :",
# datftemp$SiteID[yy]))
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = NA,
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
}
else if(as.numeric(datftemp$LabelChannel[yy]) == 0){
posn <- Position[yy-1]
pos <- posn + (datftemp$Position[yy]-datftemp$Position[yy-1])
datt<-cbind(datftemp[yy,1:6],
chromosome=chrom,
chromosomePosition=pos,
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
else{
print("Inappropriate label")
}
}
} else{ print("No cmap ID")}
if(returnMethod == "Text"){
write.table(datFinal, file.path(hmdir, paste0("Contigs_",
cmapID, "_q.cmap")),
sep = "\t",row.names = FALSE)
}else if(returnMethod == "dataFrame"){
return(datFinal)
}else{stop("No returnMethodSpecified")}
#return(datFinal)
}
#' Liftover of molecule methylation and nick label position to contig coordinates
#'
#' @param molcmap character. molecule cmap data.
#' @param outputType character. Output method. dataframe or text.
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @return dataframe containing the molecule file, with the reference position
#' @examples
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' modxmap <- readingXmap(xmap)
#' modMolcmap <- modmolcmap(molcmap = modcmap,
#' xmapdata = modxmap,
#' cntNick = 1,
#' cntMeth=2)
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
#' Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
#' refxmapdat <- readingXmap(refcontigXmap)
#' refcmapdat <- readingCmap(refCmap)
#' contigcmapdat <- readingCmap(Contigqcmap)
#' nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat,
#' contigcmap = contigcmapdat, contigID = 6701,
#' returnMethod =c("dataFrame"), chrom = 4)
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' molcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' contigcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContig_r.cmap", package="methometR")
#' contigID = 6701; cntNick = 1; cntMeth=2
#' contigmodcmap <- readingXmap(contigcmap)
#' modmolcmapNick <-molNickLoc(nickrefLoc = nickRef,
#' molcmap = modMolcmap,
#' xmapdata = modxmap,
#' contigID = contigID, cntNick = cntNick,
#' cntMeth = cntMeth)
#' MethylContigLoc<-molMethylLoc(molcmap = modmolcmapNick,
#' outputType = c("dataframe"),
#' cntNick = cntNick,
#' cntMeth = cntMeth)
#' @import utils
#' @export
molMethylLoc <- function(molcmap, outputType = c("dataframe", "text"), cntMeth, cntNick){
print("Searching for corresponding methylation label locations in the contig")
molcmap = molcmap
dataContig <- data.frame()
datFinalmol = molcmap
cmapID<-as.character(unique(datFinalmol$CMapId))
#print(paste("cmapID::",cmapID))
###Adding the probable location of Methylation
#datcontig<-data.frame()
'cores=detectCores()
cl <- makeCluster(5) #not to overload your computer
print(cl)
registerDoParallel(cl)'
#dataContig <- foreach(ti=1:length(cmapID), .combine=rbind) %dopar% {
for ( ti in 1:length(cmapID)){
'print(paste("ti", ti))
print(paste("cmapID", cmapID[ti]))'
datcontig<-data.frame()
datcontig<-datFinalmol[which(as.numeric(datFinalmol$CMapId) == as.numeric(cmapID[ti])),]
orientMolecule <- unique(as.character(datcontig$OrientationMolecule))
#print(orientMolecule)
datcontig[is.na(datcontig)]<-0
for( y in 1:nrow(datcontig)){
z=y-1
x=y+1
#print(paste("y", y))
if(y == 1){
if((datcontig$LabelChannel[y] == cntMeth
& datcontig$contigPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x]>0)){
if(orientMolecule == "+"){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}
else if((datcontig$LabelChannel[y]== cntMeth
& datcontig$contigPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y]== cntMeth & (datcontig$LabelChannel[x] == cntMeth & datcontig$contigPosition[x]==0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
##print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x]>0)){
if(orientMolecule == "+"){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}
else if((datcontig$LabelChannel[y]== cntNick
& datcontig$contigPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y]== cntNick
& (datcontig$LabelChannel[x] == cntMeth
& datcontig$contigPosition[x]==0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
##print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if (datcontig$LabelChannel[y] == cntNick & datcontig$contigPosition[y]>0){
datcontig$contigPosition[y] = datcontig$contigPosition[y]
}
else {
datcontig$contigPosition[y]=0
}
}
else{
if(datcontig$LabelChannel[y] == cntMeth
& (datcontig$LabelChannel[z] == cntNick
& datcontig$contigPosition[z]>0)){
'if(orientMolecule == "+"){'
'datcontig$contigLeft[y] <- as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))'
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:nrow(datcontig)]))
posn <- as.numeric(datcontig$Position[y+1:nrow(datcontig)])
contposn <- as.numeric(datcontig$contigPosition[y+1:nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (
(
(as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))/(as.numeric(posn[x]) - as.numeric(datcontig$Position[z])))* (contposn[x] - datcontig$contigPosition[z]))+ datcontig$contigPosition[z]
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
'if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}'
'} else{
datcontig$contigLeft[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[z])-as.numeric(datcontig$Position[y]))
g1<-grep(cntNick, as.character(datcontig$LabelChannel[(y+1):length(datcontig$LabelChannel)]))
posn <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x]>0 & datcontig$contigPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigRight[y] = as.numeric(contposn[x]) - (as.numeric(posn[x])-as.numeric(datcontig$Position[y]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigRight[y] = as.numeric(contposn[x]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[x]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}'
}
else if(datcontig$LabelChannel[y] == cntMeth &
(datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x]>0)){
g1<-grep(cntNick, as.character(datcontig$LabelChannel[1:z]))
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
ji= length(g1)
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(datcontig$Position[x]) - as.numeric(posn[z])))* (datcontig$contigPosition[x] - contposn[z])) + contposn[z]
ji= -1
}
else{
ji=ji-1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
'if(orientMolecule == "+"){
#datcontig$contigRight[y]=as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
} else{
datcontig$contigRight[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[y])-as.numeric(datcontig$Position[x]))
g1<-grep("1",as.character(datcontig$LabelChannel[1:z]))
ji= length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z]>0 & datcontig$contigPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigLeft[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[z]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigLeft[y] = as.numeric(contposn[z]) - (as.numeric(posn[z])-as.numeric(datcontig$Position[y]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji = -1
}
else{
ji=ji - 1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}
'
}
else if(datcontig$LabelChannel[y] == cntMeth
& ((datcontig$LabelChannel[z] == cntNick
| datcontig$LabelChannel[x] == cntNick)
& (datcontig$contigPosition[z] == 0
|datcontig$contigPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
#print(ji)
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$contigPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{
datcontig$contigPosition[y] = datcontig$contigPosition[y]
}
} else if((datcontig$contigPosition[y] == 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < contposn[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntMeth &
((datcontig$LabelChannel[z] == cntMeth
| datcontig$LabelChannel[x]== cntMeth)
& (datcontig$contigPosition[z]==0
|datcontig$contigPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$contigPosition[y]=0
ji = ji-1
# print(paste("2:",ji))
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else if((datcontig$contigPosition[y] == 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < contposn[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
} else if(datcontig$LabelChannel[y] == cntNick
& ((datcontig$LabelChannel[z] == cntNick
| datcontig$LabelChannel[x] == cntNick)
& (datcontig$contigPosition[z] == 0
|datcontig$contigPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$contigPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{
datcontig$contigPosition[y] = datcontig$contigPosition[y]
}
} else if((datcontig$contigPosition[y] == 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < contposn[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[z] == cntNick
& datcontig$contigPosition[z]>0)){
'if(orientMolecule == "+"){'
'datcontig$contigLeft[y] <- as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))'
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:nrow(datcontig)]))
posn <- as.numeric(datcontig$Position[y+1:nrow(datcontig)])
contposn <- as.numeric(datcontig$contigPosition[y+1:nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (
(
(as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))/(as.numeric(posn[x]) - as.numeric(datcontig$Position[z])))* (contposn[x] - datcontig$contigPosition[z]))+ datcontig$contigPosition[z]
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
'if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}'
'} else{
datcontig$contigLeft[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[z])-as.numeric(datcontig$Position[y]))
g1<-grep(cntNick, as.character(datcontig$LabelChannel[(y+1):length(datcontig$LabelChannel)]))
posn <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x]>0 & datcontig$contigPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigRight[y] = as.numeric(contposn[x]) - (as.numeric(posn[x])-as.numeric(datcontig$Position[y]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigRight[y] = as.numeric(contposn[x]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[x]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}'
}
else if(datcontig$LabelChannel[y] == cntNick &
(datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x]>0)){
g1<-grep(cntNick, as.character(datcontig$LabelChannel[1:z]))
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
ji= length(g1)
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(datcontig$Position[x]) - as.numeric(posn[z])))* (datcontig$contigPosition[x] - contposn[z])) + contposn[z]
ji= -1
}
else{
ji=ji-1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
'if(orientMolecule == "+"){
#datcontig$contigRight[y]=as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
} else{
datcontig$contigRight[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[y])-as.numeric(datcontig$Position[x]))
g1<-grep("1",as.character(datcontig$LabelChannel[1:z]))
ji= length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z]>0 & datcontig$contigPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigLeft[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[z]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigLeft[y] = as.numeric(contposn[z]) - (as.numeric(posn[z])-as.numeric(datcontig$Position[y]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji = -1
}
else{
ji=ji - 1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}
'
}
else if(datcontig$LabelChannel[y] == cntNick &
((datcontig$LabelChannel[z] == cntMeth
| datcontig$LabelChannel[x]== cntMeth)
& (datcontig$contigPosition[z]==0
|datcontig$contigPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$contigPosition[y]=0
ji = ji-1
# print(paste("2:",ji))
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else if((datcontig$contigPosition[y] == 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < contposn[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}else if (datcontig$LabelChannel[y] == cntNick & datcontig$contigPosition[y]>0){
datcontig$contigPosition[y]=datcontig$contigPosition[y]
}else{
datcontig$contigPosition[y]=0
}
}
if(datcontig$contigPosition[y] == 0
& datcontig$LabelChannel[y] == 2){
#print(paste("CMapID", cmapID[ti], "y:", y, sep = ""))
'print(y)
print(datcontig$contigPosition[y])'
}else{
}
}
dataContig<-rbind(dataContig,datcontig,row.names = NULL)
}
#stopImplicitCluster(cl)
'if(outputType == "text"){
fname=paste("Contig_",contigID[ii],"MethPositions.txt",sep="")
#rownames(datacontig)<-NULL
print(file.path(hmdir,fname,fsep=""))
write.table(dataContig,file.path(hmdir,fname,fsep="/"),row.names=FALSE)
}
else{return(dataContig)}'
return(dataContig)
}
#' Liftover of molecule methylation and nick contig position to reference coordinates
#'
#' @param molcmap character. molecule cmap data.
#' @param outputType character. Output method. dataframe or text.
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @return dataframe containing the methyl label positions mapped to the reference.
#' @examples
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' modxmap <- readingXmap(xmap)
#' modMolcmap <- modmolcmap(molcmap = modcmap,
#' xmapdata = modxmap,
#' cntNick = 1,
#' cntMeth=2)
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
#' Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
#' refxmapdat <- readingXmap(refcontigXmap)
#' refcmapdat <- readingCmap(refCmap)
#' contigcmapdat <- readingCmap(Contigqcmap)
#' nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat,
#' contigcmap = contigcmapdat, contigID = 6701,
#' returnMethod =c("dataFrame"), chrom = 4)
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' molcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' contigcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContig_r.cmap", package="methometR")
#' contigID = 6701; cntNick = 1; cntMeth=2
#' contigmodcmap <- readingXmap(contigcmap)
#' modmolcmapNick <-molNickLoc(nickrefLoc = nickRef,
#' molcmap = modMolcmap,
#' xmapdata = modxmap,
#' contigID = contigID, cntNick = cntNick,
#' cntMeth = cntMeth)
#' MethylRefLoc<-molMethylRefLoc(molcmap = modmolcmapNick,
#' outputType = c("dataframe"),
#' cntNick = cntNick,
#' cntMeth = cntMeth)
#' @import utils
#' @export
molMethylRefLoc <- function(molcmap, outputType = c("dataframe", "text"), cntMeth = 1, cntNick = 2){
print("Searching for the methylation label locations in the reference")
molcmap = molcmap
#molcmap = molcmapFinal
dataContig <- data.frame()
datFinalmol = molcmap
cmapID<-as.character(unique(datFinalmol$CMapId))
#print(paste("cmapID::",cmapID))
###Adding the probable location of Methylation
#datcontig<-data.frame()
'cores=detectCores()
cl <- makeCluster(5) #not to overload your computer
print(cl)
registerDoParallel(cl)'
#dataContig <- foreach(ti=1:length(cmapID), .combine=rbind) %dopar% {
for ( ti in 1:length(cmapID)){
#print(paste("ti", ti))
datcontig<-data.frame()
#datcontig<-datFinalmol[which(as.numeric(datFinalmol$CMapId)== cmapID[ti]),]
datcontig<-datFinalmol[which(as.numeric(datFinalmol$CMapId)== as.numeric(cmapID[ti])),]
orientMolecule <- unique(as.character(datcontig$OrientationMolecule))
#print(orientMolecule)
datcontig[is.na(datcontig)]<-0
for( y in 1:nrow(datcontig)){
z=y-1
x=y+1
#print(paste("y", y))
if(y == 1){
if(datcontig$LabelChannel[y] == cntMeth
& (datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x]>0)){
if(orientMolecule == "+"){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}
else if((datcontig$LabelChannel[y]== cntMeth
& datcontig$chromPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y]== cntMeth
& (datcontig$LabelChannel[x] == cntMeth
& datcontig$chromPosition[x]==0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x]>0)){
if(orientMolecule == "+"){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}
else if((datcontig$LabelChannel[y]== cntNick
& datcontig$chromPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[x] == cntMeth
& datcontig$chromPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if (datcontig$LabelChannel[y] == cntNick & datcontig$chromPosition[y]>0){
datcontig$chromPosition[y] = datcontig$chromPosition[y]
}
else {
datcontig$chromPosition[y]=0
}
}
else{
if(datcontig$LabelChannel[y] == cntMeth
& (datcontig$LabelChannel[z] == cntNick
& datcontig$chromPosition[z]>0)){
'if(orientMolecule == "+"){'
'datcontig$contigLeft[y] <- as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))'
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:nrow(datcontig)]))
posn <- as.numeric(datcontig$Position[y+1:nrow(datcontig)])
contposn <- as.numeric(datcontig$chromPosition[y+1:nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (
(
(as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))/(as.numeric(posn[x]) - as.numeric(datcontig$Position[z])))* (contposn[x] - datcontig$chromPosition[z]))+ datcontig$chromPosition[z]
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
'if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}'
'} else{
datcontig$contigLeft[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[z])-as.numeric(datcontig$Position[y]))
g1<-grep(cntNick, as.character(datcontig$LabelChannel[(y+1):length(datcontig$LabelChannel)]))
posn <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x]>0 & datcontig$chromPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigRight[y] = as.numeric(contposn[x]) - (as.numeric(posn[x])-as.numeric(datcontig$Position[y]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigRight[y] = as.numeric(contposn[x]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[x]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}'
}
else if(datcontig$LabelChannel[y] == cntMeth &
(datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x]>0)){
g1<-grep(cntNick, as.character(datcontig$LabelChannel[1:z]))
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
ji= length(g1)
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(datcontig$Position[x]) - as.numeric(posn[z])))* (datcontig$chromPosition[x] - contposn[z])) + contposn[z]
ji= -1
}
else{
ji=ji-1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
'if(orientMolecule == "+"){
#datcontig$contigRight[y]=as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
} else{
datcontig$contigRight[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[y])-as.numeric(datcontig$Position[x]))
g1<-grep("1",as.character(datcontig$LabelChannel[1:z]))
ji= length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z]>0 & datcontig$chromPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigLeft[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[z]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigLeft[y] = as.numeric(contposn[z]) - (as.numeric(posn[z])-as.numeric(datcontig$Position[y]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji = -1
}
else{
ji=ji - 1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}
'
}
else if(datcontig$LabelChannel[y] == cntMeth
& ((datcontig$LabelChannel[z] == cntNick
| datcontig$LabelChannel[x] == cntNick)
& (datcontig$chromPosition[z] == 0
|datcontig$chromPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$chromPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{
datcontig$chromPosition[y] = datcontig$chromPosition[y]
}
} else if((datcontig$chromPosition[y] == 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < contposn[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntMeth &
((datcontig$LabelChannel[z] == cntMeth
| datcontig$LabelChannel[x]== cntMeth)
& (datcontig$chromPosition[z]==0
|datcontig$chromPosition[x]==0))){g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$chromPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else if((datcontig$chromPosition[y] == 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < contposn[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[z] == cntNick
& datcontig$chromPosition[z]>0)){
'if(orientMolecule == "+"){'
'datcontig$contigLeft[y] <- as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))'
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:nrow(datcontig)]))
posn <- as.numeric(datcontig$Position[y+1:nrow(datcontig)])
contposn <- as.numeric(datcontig$chromPosition[y+1:nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (
(
(as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))/(as.numeric(posn[x]) - as.numeric(datcontig$Position[z])))* (contposn[x] - datcontig$chromPosition[z]))+ datcontig$chromPosition[z]
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
'if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}'
'} else{
datcontig$contigLeft[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[z])-as.numeric(datcontig$Position[y]))
g1<-grep(cntNick, as.character(datcontig$LabelChannel[(y+1):length(datcontig$LabelChannel)]))
posn <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x]>0 & datcontig$chromPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigRight[y] = as.numeric(contposn[x]) - (as.numeric(posn[x])-as.numeric(datcontig$Position[y]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigRight[y] = as.numeric(contposn[x]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[x]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}'
}
else if(datcontig$LabelChannel[y] == cntNick &
(datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x]>0)){
g1<-grep(cntNick, as.character(datcontig$LabelChannel[1:z]))
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
ji= length(g1)
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(datcontig$Position[x]) - as.numeric(posn[z])))* (datcontig$chromPosition[x] - contposn[z])) + contposn[z]
ji= -1
}
else{
ji=ji-1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
'if(orientMolecule == "+"){
#datcontig$contigRight[y]=as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
} else{
datcontig$contigRight[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[y])-as.numeric(datcontig$Position[x]))
g1<-grep("1",as.character(datcontig$LabelChannel[1:z]))
ji= length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z]>0 & datcontig$chromPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigLeft[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[z]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigLeft[y] = as.numeric(contposn[z]) - (as.numeric(posn[z])-as.numeric(datcontig$Position[y]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji = -1
}
else{
ji=ji - 1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}
'
}
else if(datcontig$LabelChannel[y] == cntNick
& ((datcontig$LabelChannel[z] == cntNick
| datcontig$LabelChannel[x] == cntNick)
& (datcontig$chromPosition[z] == 0
|datcontig$chromPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$chromPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{
datcontig$chromPosition[y] = datcontig$chromPosition[y]
}
} else if((datcontig$chromPosition[y] == 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
' print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < contposn[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntNick &
((datcontig$LabelChannel[z] == cntMeth
| datcontig$LabelChannel[x]== cntMeth)
& (datcontig$chromPosition[z]==0
|datcontig$chromPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$chromPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else if((datcontig$chromPosition[y] == 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < contposn[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if (datcontig$LabelChannel[y] == cntNick & datcontig$chromPosition[y]>0){
datcontig$chromPosition[y]=datcontig$chromPosition[y]
}
else{
datcontig$chromPosition[y]=0
}
}
}
dataContig<-rbind(dataContig,datcontig,row.names = NULL)
}
#stopImplicitCluster(cl)
'if(outputType == "text"){
fname=paste("Contig_",contigID[ii],"MethPositions.txt",sep="")
#rownames(datacontig)<-NULL
print(file.path(hmdir,fname,fsep=""))
write.table(dataContig,file.path(hmdir,fname,fsep="/"),row.names=FALSE)
}
else{return(dataContig)}'
return(dataContig)
}
#' Extracting contig information
#'
#' @param contigRefxmap character. Contig xmap data.
#' @param chrom character. Chromosome of interest.
#' @param startPos integer.Start position.
#' @param endPos integer. End position.
#' @return dataframe with data extracted from xmap.
#' @examples
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' modxmap <- readingXmap(refcontigXmap)
#' extractedInfo<-contigextract(contigRefxmap = modxmap, chrom = 4, startPos = 100000, endPos = 200000)
#' @import utils
#' @export
contigextract <- function(contigRefxmap, chrom, startPos, endPos){
print("Extracting Contig information")
if(startPos > 0 & endPos > 0 & chrom >0){
dat1 <- contigRefxmap[which(contigRefxmap$RefStartPos <= startPos
& contigRefxmap$RefEndPos >= endPos
& contigRefxmap$RefContigID == chrom ),]
}else if(startPos > 0 & endPos == 0 & chrom >0){
dat1 <- contigRefxmap[which(contigRefxmap$RefStartPos <= startPos
& contigRefxmap$RefEndPos >= startPos
& contigRefxmap$RefContigID == chrom ),]
}else if(startPos == 0 & endPos == 0 & chrom >0){
dat1 <- contigRefxmap[which(contigRefxmap$RefContigID == chrom ),]
}else{
print("chromosome or start or end information required!!")
}
contigID <- dat1$QryContigID
chrom <- unique(dat1$RefContigID)
dat <- data.frame(contigID = contigID, chrom = rep(chrom, length(contigID)))
return(dat)
}
#' Main function to call the extraction, modification and quantification process.
#'
#' @param cmaploc_mol character. path to the cmap folder.
#' @param untar boolean. untar option. True or False/
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @param selectedRegion boolean. if TRUE, selected region is analyzed and
#' the user provides chromosome and start and end point. If FALSE, whole
#' genome analysed.
#' @param chrom character. Chromosome number if selectedRegion is TRUE
#' @param startPos integer. Start of the query if selectedRegion is TRUE
#' @param endPos integer. End of the query if selectedRegion is TRUE
#' @param outputFormat Character. Choices are individualText, multipleText and
#' dataframe.
#' @param path Character. Path of the folder where log files needs to be written
#' to.
#' @param logFilename character. Log file name.
#' @return dataframe or text files containing the modified files.
#' @examples
#'\dontrun{
#' molcmap <- system.file("extdata", "SampMolecule.cmap", package="methometR")
#' cmap <- system.file("extdata", "SampContig.cmap", package="methometR")
#' bed<-molMethylRefLoc(nickrefLoc,molcmap,xmapdata, contigID, cntNick ,
#' cntMeth)
#'}
#' @import utils
#' @import logr
#' @export
extracting_modifying_methLabels <- function(cmaploc_mol,
untar = FALSE, cntNick, cntMeth, selectedRegion = TRUE, chrom, startPos, endPos,
outputFormat = c("individualText", "multipleText",
"dataFrame"), path, logFilename){
#logFilename = ""
logFilename = logFilename
ifelse(logFilename == "",
log_open(file.path(path, "logmethometR.txt")),
log_open(file.path(path, logFilename)))
log_print("----methometr Package----")
print("----Function to map nick and methylation label to reference----")
log_print("----Function to map nick and methylation label to reference----")
cntNick =cntNick; cntMeth = cntMeth;
untar = untar; cmaploc_mol = cmaploc_mol;
selectedRegion = selectedRegion;
outputFormat = outputFormat;
path = path
refcmap <- data.frame();
querycmap <- data.frame();contigRefxmap <- data.frame()
if(untar == TRUE){
print("---Untaring and reading molecule and contig info---")
log_print("---Untaring and reading molecule and contig info---")
untaringdirectoy(cmaploc_mol)
st <- strsplit(cmaploc_mol, split = ".zip")
cmapPath <- st[[1]][1]
##contig and reference maps
print("Extracting file paths for required contig and reference files")
contigRefpath <- file.path(cmapPath, "output/contigs/exp_refineFinal1_sv/merged_smaps/")
contRefXmappath <- list.files(contigRefpath, pattern = "*.xmap", full.names = TRUE)
Refcmappath <- list.files(contigRefpath, pattern = "*_r.cmap", full.names = TRUE)
Querycmappath <- list.files(contigRefpath, pattern = "*_q.cmap", full.names = TRUE)
print("Reading contig, molecule and reference xmap")
refcmap <- readingCmap(Refcmappath)
querycmap <- readingCmap(Querycmappath)
contigRefxmap <- readingXmap(xmap = contRefXmappath)
chrom1 <- unique(contigRefxmap$RefContigID)
##contig and molecule maps
contigMolPath <- file.path(cmapPath, "output/contigs/exp_refineFinal1/alignmol/merge/")
lmolecules <- list.files(cmaploc_mol, pattern = "*.xmap", full.names = FALSE)
st1 <- strsplit(lmolecules, split = "contig")
st2 <- sapply(st1, "[[", 2)
st3 <- strsplit(st2, split = "\\.")
contigID <- sapply(st3, "[[", 1)
lcontig <- list.files(cmaploc_mol, pattern = "*_r.cmap", full.names = TRUE)
lxmap <- list.files(cmaploc_mol, pattern = "*.", full.names = TRUE)
}
else {
print("---Reading molecule and contig info---")
log_print("---Reading molecule and contig info---")
##contig and reference maps
print("Extracting file paths for required contig and reference files")
contigRefpath <- file.path(cmaploc_mol, "output/contigs/exp_refineFinal1_sv/merged_smaps/")
contRefXmappath <- list.files(contigRefpath, pattern = "*.xmap", full.names = TRUE)
Refcmappath <- list.files(contigRefpath, pattern = "*_r.cmap", full.names = TRUE)
Querycmappath <- list.files(contigRefpath, pattern = "*_q.cmap", full.names = TRUE)
print("Reading contig, molecule and reference xmap")
refcmap <- readingCmap(Refcmappath)
querycmap <- readingCmap(Querycmappath)
contigRefxmap <- readingXmap(xmap = contRefXmappath)
chrom1 <- unique(contigRefxmap$RefContigID)
##contig and molecule maps
contigMolPath <- file.path(cmaploc_mol, "output/contigs/exp_refineFinal1/alignmol/merge")
lmolecules <- list.files(contigMolPath, pattern = "*.xmap", full.names = FALSE)
st1 <- strsplit(lmolecules, split = "contig")
st2 <- sapply(st1, "[[", 2)
st3 <- strsplit(st2, split = "\\.")
contigID <- sapply(st3, "[[", 1)
}
datmolInfo <- data.frame()
if(selectedRegion == FALSE){
modmol <- data.frame()
print("Selected region is FALSE")
'pp <- paste("Total number of contigs to be processed:", length(contigID))
log_print(pp)
print(paste("Total number of contigs to be processed:", length(contigID)))'
chrom <- sort(chrom1)
for(uu in seq_along(chrom)){
datcont <- contigRefxmap[which(contigRefxmap$RefContigID == chrom[uu]),]
contigID <- datcont$QryContigID
pa <- paste("---Processing Chromosome",
paste("chr_", chrom[uu], sep = ""),
"--", sep = "")
print(pa)
log_print(pa)
pa1 <- paste("---Number of contigs for chromosme ",
paste("chr_", chrom[uu], sep = ""), ":",
length(contigID), "---", sep = "")
#pp1 <- paste("---Number of contigs for chromosme1:", length(contigID))
print(pa1)
log_print(pa1)
if(dir.exists(file.path(path, paste("chr_", chrom[uu], sep = "")))
& length(list.files(path = file.path(path, paste("chr_", chrom[uu], sep = "")))) > 0){
pa7 <- paste("chr_", chrom[uu],": already processed", sep = "")
log_print(pa7)
next;
}else if(!dir.exists(file.path(path, paste("chr_", chrom[uu], sep = "")))){
pp2 <- paste("---Creating directory for Chromosome", chrom[uu], "--", sep = "")
print(paste("---Creating directory for Chromosome", chrom[uu], "--", sep = ""))
log_print(pp2)
dir.create(file.path(path, paste("chr_", chrom[uu], sep = "")))
outpath <- file.path(path, paste("chr_", chrom[uu], sep = ""))
}else{
outpath <- file.path(path, paste("chr_", chrom[uu], sep = ""))
}
if(length(contigID) > 1){
for (ii in seq_along(contigID)){
contigRefxmap = contigRefxmap;refcmap = refcmap
#for (ii in 803:length(contigID)){
print(paste("Contig being analyzed:", contigID[ii], sep = ""))
pp5 <- paste("Contig being analyzed:", contigID[ii], sep = "")
log_print(pp5)
print("Reading contig, molecule and reference xmap")
contigmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],"_r.cmap",sep = ""), full.names = TRUE)
molmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap",sep = ""), full.names = TRUE)
xmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],".xmap",sep = ""), full.names = TRUE)
#contigdat <- readingCmap(contigmap)
if(molmap == ""){
print(paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap", "is discarded from analysis!!!"))
pp4 <- paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap", "is discarded from analysis!!!")
log_print(pp4)
next;
}else{
moldat <- readingCmap(molmap)
}
dat1_t <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]),]
if((nrow(dat1_t) > 1)
& (length(unique(dat1_t$RefContigID)) > 1)){
message("Work in progress translocation function")
next;
}else{
dat1 <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]
& contigRefxmap$RefContigID == chrom[uu]),]
}
xmapdat <- readingXmap(xmap)
if(all(is.na((moldat[1:3,]))) == TRUE
| all(is.na((xmapdat[1:3,]))) == TRUE
| all(is.na((querycmap[1:3,]))) == TRUE){
log_print("Either xmap,molecule cmap or reference cmap file empty !!!!")
print("Either xmap,molecule cmap or reference cmap file empty !!!!")
next;
}else{moldat = moldat; xmapdat = xmapdat}
if(nrow(dat1) >= 1){
contigID[ii] = contigID[ii]
#chrom = unique(dat1$RefContigID)
#chrom2 = unique(dat1$RefContigID)
#modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
'if(length(chrom2) > 1){
nickrefLoc <- data.frame()
for(oo in 1:length(chrom2)){
nickrefLoc1 <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom2[oo],
returnMethod = "dataFrame")
nickrefLoc <- rbind(nickrefLoc, nickrefLoc1,row.names = NULL)
}
}else{
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom2,
returnMethod = "dataFrame")
}'
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom[uu],
returnMethod = "dataFrame")
modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
methylNickLoc <- molNickLoc(nickrefLoc = nickrefLoc,
molcmap = modmolCmapdat,
xmapdata = xmapdat,
contigID = contigID[ii],
cntNick = cntNick,
cntMeth = cntMeth)
molcmapFinal <- molMethylLoc(methylNickLoc, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
molcmapFinal1 <- molMethylRefLoc(molcmapFinal, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
print (outpath)
if(outputFormat == "individualText"){
write.table(molcmapFinal1, file.path(outpath, paste("modifiedMol_", contigID[ii], ".txt", sep = "")))
}else if(outputFormat == "dataFrame"){
modmol <- rbind(modmol,molcmapFinal1, row.names = NULL)
}else if(outputFormat == "multipleText"){
modmol <- rbind(modmol,molcmapFinal1, row.names = NULL)
print("Will print outside the loop")
}else{stop("outputMethod Incorrect!!!!")}
}else{ print(paste("Contig:", contigID[ii], " is absent."))
next;}
}
}else{
chrom = chrom1
datcont <- contigRefxmap[which(contigRefxmap$RefContigID == chrom),]
contigID <- datcont$QryContigID
pa <- paste("---Processing Chromosome",
paste("chr_", chrom, sep = ""),
"--", sep = "")
print(pa)
log_print(pa)
pa1 <- paste("---Number of contigs for chromosme ",
paste("chr_", chrom, sep = ""), ":",
length(contigID), "---", sep = "")
#pp1 <- paste("---Number of contigs for chromosme1:", length(contigID))
print(pa1)
log_print(pa1)
pp6 <- (paste("Contig being analyzed:", contigID, sep = ""))
print(pp6)
log_print(pp6)
if(dir.exists(file.path(path, paste("chr_", chrom, sep = "")))
& length(list.files(path = file.path(path, paste("chr_", chrom, sep = "")))) > 0){
pa7 <- paste("chr_", chrom,": alreay processed", sep = "")
log_print(pa7)
next;
}else if(!dir.exists(file.path(path, paste("chr_", chrom, sep = "")))){
pp2 <- paste("---Creating directory for Chromosome", chrom, "--", sep = "")
print(paste("---Creating directory for Chromosome", chrom, "--", sep = ""))
log_print(pp2)
dir.create(file.path(path, paste("chr_", chrom, sep = "")))
outpath <- file.path(path, paste("chr_", chrom, sep = ""))
}else{
outpath <- file.path(path, paste("chr_", chrom, sep = ""))
}
'dat1 <- refxmap[which(refxmap$QryContigID == contigID),]
chrom = unique(dat1$RefContigID)'
contigmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,"_r.cmap",sep = ""), full.names = TRUE)
molmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,"_q.cmap",sep = ""), full.names = TRUE)
xmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,".xmap",sep = ""), full.names = TRUE)
#contigdat <- readingCmap(contigmap)
if(molmap == NA){
print(paste("exp_refineFinal1_contig",contigID,"_q.cmap", "is discarded from analysis!!!"))
pp4 <- paste("exp_refineFinal1_contig",contigID,"_q.cmap", "is discarded from analysis!!!")
log_print(pp4)
next;
}else{
moldat <- readingCmap(molmap)
}
xmapdat <- readingXmap(xmap = xmap)
if(is.na(moldat) == TRUE
| is.na(xmapdat) == TRUE){
log_print("Either xmap,molecule cmap or reference cmap file empty !!!!")
print("Either xmap,molecule cmap or reference cmap file empty !!!!")
next;
}else{moldat = moldat; xmapdat = xmapdat}
#dat1 <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]),]
if(nrow(dat1) >= 1){
contigID = contigID
#chrom = unique(dat1$RefContigID)
chrom2 = unique(dat1$RefContigID)
xmapdat <- readingXmap(xmap)
#modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
if(length(chrom2) > 1){
nickrefLoc <- data.frame()
for(oo in 1:length(chrom2)){
nickrefLoc1 <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID,
chrom = chrom2[oo],
returnMethod = "dataFrame")
nickrefLoc <- rbind(nickrefLoc, nickrefLoc1,row.names = NULL)
}
}else{
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID,
chrom = chrom2,
returnMethod = "dataFrame")
}
modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
methylNickLoc <- molNickLoc(nickrefLoc = nickrefLoc,
molcmap = modmolCmapdat,
xmapdata = xmapdat,
contigID = contigID,
cntNick = cntNick,
cntMeth = cntMeth)
molcmapFinal <- molMethylLoc(methylNickLoc, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
molcmapFinal1 <- molMethylRefLoc(molcmapFinal, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
print (outpath)
if(outputFormat == "individualText"){
write.table(molcmapFinal1, file.path(outpath, paste("modifiedMol_", contigID, ".txt", sep = "")))
}else if(outputFormat == "dataFrame"){
modmol <- rbind(modmol,molcmapFinal1,row.names = NULL)
}else if(outputFormat == "multipleText"){
modmol <- rbind(modmol,molcmapFinal1,row.names = NULL)
print("Will print outside the loop")
}else{stop("outputMethod Incorrect!!!!")}
}else{ print(paste("Contig:", contigID, " is absent."))
next;}
}
if(outputFormat == "multipleText"){
if(length(unique(modmol$ContigID)) > 1){
contig <- unique(modmol$ContigID)
contigname <- paste(contig, collapse = "_")
write.table(modmol, file.path(outpath, paste("modifiedMol_", contigname, ".txt", sep = "")))
}else if (length(unique(modmol$ContigID)) == 1){
print("Individual contig files have been written !!")
}else{stop("No contigs found !!!")}
}else if(outputFormat == "individualText"){
log_print("Individual contig files have already been written !!")
}else if(outputFormat == "dataFrame"){
return(modmol)
}else{stop("outputMethod Incorrect!!!!")}
pp6 <- paste("---Finished Processing", chrom[uu], "--", sep = "")
log_print(pp6)
}
}else if(selectedRegion == TRUE){
print("Selected region is TRUE")
dir.create(file.path(path, "Selected"))
chrom = chrom;
startPos = startPos; endPos = endPos;
dat1 <- contigextract(contigRefxmap = contigRefxmap,
chrom = chrom, startPos = startPos, endPos = endPos)
if(nrow(dat1) >= 1){
contigID <- dat1$contigID
chrom <- unique(dat1$chrom)
}else{stop("Selected region does not have a contig mapped to it!!!")}
print(paste("Total number of contigs to be processed:", length(contigID)))
'pp7 <- paste("---Creating directory for Chromosome", chrom, "--", sep = "")
print(paste("---Creating directory for Chromosome", chrom, "--", sep = ""))
outpath <- dir.create(file.path(path, paste("chr_", chrom[uu], sep = "")))'
if(dir.exists(file.path(path, "Selected", paste("chr_", chrom, sep = "")))
& length(list.files(path = file.path(path, paste("chr_", "Selected", chrom, sep = "")))) > 0){
pa7 <- paste("chr_", chrom,": alreay processed", sep = "")
log_print(pa7)
}else if(!dir.exists(file.path(path, "Selected", paste("chr_", chrom, sep = "")))){
pp2 <- paste("---Creating directory for Chromosome", chrom, "--", sep = "")
print(paste("---Creating directory for Chromosome", chrom, "--", sep = ""))
log_print(pp2)
dir.create(file.path(path, "Selected", paste("chr_", chrom, sep = "")))
outpath <- file.path(path, "Selected", paste("chr_", chrom, sep = ""))
}else{
outpath <- file.path(path, "Selected", paste("chr_", chrom, sep = ""))
}
if(length(contigID) > 1){
print(nrow(contigRefxmap));
print(nrow(refcmap));
for (ii in 1:length(contigID)){
#for (ii in 803:length(contigID)){
print(paste("Contig being analyzed:", contigID[ii], sep = ""))
pp5 <- paste("Contig being analyzed:", contigID[ii], sep = "")
log_print(pp5)
print("Reading contig, molecule and reference xmap")
contigmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],"_r.cmap",sep = ""), full.names = TRUE)
molmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap",sep = ""), full.names = TRUE)
xmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],".xmap",sep = ""), full.names = TRUE)
#contigdat <- readingCmap(contigmap)
if(molmap == ""){
print(paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap", "is discarded from analysis!!!"))
pp4 <- paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap", "is discarded from analysis!!!")
log_print(pp4)
next;
}else{
moldat <- readingCmap(molmap)
}
dat1 <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]),]
xmapdat <- readingXmap(xmap)
if(all(is.na((moldat[1:3,]))) == TRUE
| all(is.na((xmapdat[1:3,]))) == TRUE
| all(is.na((querycmap[1:3,]))) == TRUE){
log_print("Either xmap,molecule cmap or reference cmap file empty !!!!")
print("Either xmap,molecule cmap or reference cmap file empty !!!!")
next;
}else{moldat = moldat; xmapdat = xmapdat}
if(nrow(dat1) >= 1){
contigID[ii] = contigID[ii]
#chrom = unique(dat1$RefContigID)
chrom2 = unique(dat1$RefContigID)
#modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
if(length(chrom2) > 1){
nickrefLoc <- data.frame()
for(oo in 1:length(chrom2)){
nickrefLoc1 <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom2[oo],
returnMethod = "dataFrame")
nickrefLoc <- rbind(nickrefLoc, nickrefLoc1,row.names = NULL)
}
}else{
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom2,
returnMethod = "dataFrame")
}
modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
methylNickLoc <- molNickLoc(nickrefLoc = nickrefLoc,
molcmap = modmolCmapdat,
xmapdata = xmapdat,
contigID = contigID[ii],
cntNick = cntNick,
cntMeth = cntMeth)
molcmapFinal <- molMethylLoc(methylNickLoc, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
molcmapFinal1 <- molMethylRefLoc(molcmapFinal, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
if(outputFormat == "individualText"){
write.table(molcmapFinal1, file.path(outpath, paste("modifiedMol_", contigID[ii], ".txt", sep = "")))
}else if(outputFormat == "dataFrame"){
modmol <- rbind(modmol,molcmapFinal1, row.names = NULL)
}else if(outputFormat == "multipleText"){
modmol <- rbind(modmol,molcmapFinal1, row.names = NULL)
print("Will print outside the loop")
}else{stop("outputMethod Incorrect!!!!")}
}else{ print(paste("Contig:", contigID[ii], " is absent."))
next;}
}
}else{
print(paste("Contig being analyzed:", contigID, sep = ""))
'dat1 <- refxmap[which(refxmap$QryContigID == contigID),]
chrom = unique(dat1$RefContigID)'
contigmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,"_r.cmap",sep = ""), full.names = TRUE)
molmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,"_q.cmap",sep = ""), full.names = TRUE)
xmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,".xmap",sep = ""), full.names = TRUE)
#contigdat <- readingCmap(contigmap)
if(molmap == NA){
print(paste("exp_refineFinal1_contig",contigID,"_q.cmap", "is discarded from analysis!!!"))
pp4 <- paste("exp_refineFinal1_contig",contigID,"_q.cmap", "is discarded from analysis!!!")
log_print(pp4)
}else{
moldat <- readingCmap(molmap)
}
xmapdat <- readingXmap(xmap = xmap)
if(is.na(moldat) == TRUE
| is.na(xmapdat) == TRUE){
log_print("Either xmap,molecule cmap or reference cmap file empty !!!!")
print("Either xmap,molecule cmap or reference cmap file empty !!!!")
}else{moldat = moldat; xmapdat = xmapdat}
#dat1 <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]),]
if(nrow(dat1) >= 1){
contigID = contigID
#chrom = unique(dat1$RefContigID)
chrom2 = unique(dat1$RefContigID)
xmapdat <- readingXmap(xmap)
#modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
if(length(chrom2) > 1){
nickrefLoc <- data.frame()
for(oo in 1:length(chrom2)){
nickrefLoc1 <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID,
chrom = chrom2[oo],
returnMethod = "dataFrame")
nickrefLoc <- rbind(nickrefLoc, nickrefLoc1,row.names = NULL)
}
}else{
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID,
chrom = chrom2,
returnMethod = "dataFrame")
}
modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
methylNickLoc <- molNickLoc(nickrefLoc = nickrefLoc,
molcmap = modmolCmapdat,
xmapdata = xmapdat,
contigID = contigID,
cntNick = cntNick,
cntMeth = cntMeth)
molcmapFinal <- molMethylLoc(methylNickLoc, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
molcmapFinal1 <- molMethylRefLoc(molcmapFinal, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
if(outputFormat == "individualText"){
write.table(molcmapFinal1, file.path(outpath, paste("modifiedMol_", contigID, ".txt", sep = "")))
}else if(outputFormat == "dataFrame"){
modmol <- rbind(modmol,molcmapFinal1,row.names = NULL)
}else if(outputFormat == "multipleText"){
modmol <- rbind(modmol,molcmapFinal1,row.names = NULL)
print("Will print outside the loop")
}else{stop("outputMethod Incorrect!!!!")}
}else{ print(paste("Contig:", contigID, " is absent."))
}
}
if(outputFormat == "multipleText"){
if(length(unique(modmol$ContigID)) > 1){
contig <- unique(modmol$ContigID)
contigname <- paste(contig, collapse = "_")
write.table(modmol, file.path(outpath, paste("modifiedMol_", contigname, ".txt", sep = "")))
}else if (length(unique(modmol$ContigID)) == 1){
print("Individual contig files have been written !!")
}else{stop("No contigs found !!!")}
}else if(outputFormat == "individualText"){
log_print("Individual contig files have already been written !!")
}else if(outputFormat == "dataFrame"){
return(modmol)
}else{stop("outputMethod Incorrect!!!!")}
pp10 <- paste("---Finished Processing Selected Region---")
log_print(pp10)
}else{stop("Selected Region Not Selected!!!")}
log_print("Molecule cmaps modified !!!")
print("Molecule cmaps modified !!!")
log_print("---Closing Log Files!!!---")
log_close()
#return(paste("query methylation Labels Modified"))
#return (fname1)
}
VilainLab/methometR documentation built on Dec. 18, 2021, 6:17 p.m.
R Package Documentation
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Defines functions extracting_modifying_methLabels contigextract molMethylRefLoc molMethylLoc nickReference molNickLoc untaringdirectoy modmolcmap readingXmap readingCmap
Documented in contigextract extracting_modifying_methLabels modmolcmap molMethylLoc molMethylRefLoc molNickLoc nickReference readingCmap readingXmap untaringdirectoy
#' Reads Bionano Cmap files
#'
#' @param cmap character. Path to Bionano cmap file.
#' @return Data Frame Contains the cmap file information.
#' @examples
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' @import utils
#' @export
readingCmap <- function(cmap){
#Reading contig, molecule or reference cmap
cmap_temp<-file(cmap, "r")
cmap_temp1<-readLines(cmap_temp, n = -1)
close(cmap_temp)
g1 <- grep("#h", cmap_temp1)
g2 <- grep("#f ",cmap_temp1)
##Extracting data
if (g1+1 == g2){
##reading the cmap file
dat <- gsub("#h ", "", cmap_temp1)
#dat4 <- textConnection(dat[g1:length(dat)])
dat4 <- textConnection(dat[g1])
r1 <- read.table(dat4, sep = "\t",header=FALSE)
#dat4 <- textConnection(dat[g1:length(dat)])
g3<-g1+2
dat5 <- textConnection(dat[g3:length(dat)])
r2 <- read.table(dat5, sep = "\t",header=FALSE)
close(dat5)
r8 <- data.frame(r2)
nam <- tryCatch(
names(r8) <- as.character(unlist(r1)),
warning = function(w) {
print(paste("File:", cmap, "is empty"))
return (NA)
},
error = function(e) {
print(paste("File:", cmap, "is empty"))
return (NA)
}
)
###Returning the dara
if (length(nam) == 0){
return(NA)
}
else{
names(r8) <- nam
return(r8)
}
}
return(r8)
}
#' Reads Bionano xmap files
#'
#' @param xmap character. Path to Bionano xmap file.
#' @return Data Frame Contains the xmap file information.
#' @examples
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' modxmap <- readingXmap(xmap)
#' @import utils
#' @export
readingXmap <- function(xmap) {
##Reading contig-molecule or reference-contig xmap
xmap = xmap
conXmap <- file(xmap, "r")
r10 <- readLines(conXmap, n = -1)
close(conXmap)
datfinal <- data.frame()
g1 <- grep("#h ", r10)
g2 <- grep("#f ", r10)
##Reading contig xmap
if (g1+1 == g2){
dat <- gsub("#h ", "", r10)
#dat4 <- textConnection(dat[g1:length(dat)])
dat4 <- textConnection(dat[g1])
r1 <- read.table(dat4, sep = "\t",header=FALSE)
#dat4 <- textConnection(dat[g1:length(dat)])
g3<-g1+2
dat5 <- textConnection(dat[g3:length(dat)])
r2 <- read.table(dat5, sep = "\t",header=FALSE)
#r8<-data.frame(r2)
nam <- tryCatch(
names(r2) <- as.character(unlist(r1)),
warning = function(w) {
print(paste("File:", xmap, "is empty"))
return (NA)
},
error = function(e) {
print(paste("File:", xmap, "is empty"))
return (NA)
}
)
##Returning the data
if (length(nam) == 0){
return(NA)
}
else{
names(r2) <- nam
return(r2)
}
}
return(r2)
}
#' Identifies and documents the methylation and nick labels
#'
#' @param molcmap character. Path to Bionano molecule cmap.
#' @param xmapdata character. Path to Bionano molecule contig xmap.
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @return Data Frame with the molecule cmap, with the exact site number
#' for methylation and nick labels.
#' @examples
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' modxmap <- readingXmap(xmap)
#' modMolcmap <- modmolcmap(molcmap = modcmap,
#' xmapdata = modxmap,
#' cntNick = 1,
#' cntMeth=2)
#' @import utils
#' @export
modmolcmap <- function(molcmap, xmapdata, cntNick , cntMeth ){
print("Adding the label location to molecule files")
molCmapID <- as.numeric(unique(molcmap$CMapId))
dataContig<-data.frame()
datf<-data.frame()
datFinalmol <- data.frame()
xmapdata = xmapdata
molcmap = molcmap
cntNick = cntNick
cntMeth = cntMeth
###counting nick and methylation region in the molcmap
for (j in seq_along(molCmapID)){
#print(molCmapID[j])
dat3<-molcmap[which(molcmap$CMapId==molCmapID[j] &
(molcmap$LabelChannel == cntNick
| molcmap$LabelChannel == cntMeth)),]
datnick <- dat3[which(dat3$LabelChannel == cntNick),]
datmeth <- dat3[which(dat3$LabelChannel == cntMeth),]
orientMol <- c()
countnick <- c()
countmeth <- c()
molxmap <- xmapdata[which(xmapdata$QryContigID == molCmapID[j]),]
dat4 <- molcmap[which(molcmap$CMapId==molCmapID[j]
& molcmap$LabelChannel == 0),]
dat4 <- cbind(dat4[,1:4],
NickLoc = "-",
MethLoc = "-",
OrientationMolecule = molxmap$Orientation,
dat4[,5:ncol(dat4)],
row.names = NULL)
cntnickneg = nrow(datnick) + 1; cntmethneg = nrow(datmeth) + 1
orient <- unique(as.character(molxmap$Orientation))
cntnickpos = 0; cntmethpos = 0
for (hh in 1:nrow(dat3)){
if(as.numeric(dat3$LabelChannel[hh])== cntNick){
cntnickpos = cntnickpos + 1
#print(paste("hh:", hh, "cntnickpos:", cntnickpos))
countnick<-c(countnick,cntnickpos)
orientMol <- c(orientMol, orient)
countmeth<-c(countmeth,0)
}
else if(as.numeric(dat3$LabelChannel[hh])== cntMeth){
cntmethpos = cntmethpos + 1
countmeth<-c(countmeth,cntmethpos)
orientMol <- c(orientMol, orient)
countnick<-c(countnick,0)
}
else {
countmeth<-c(countmeth,0)
countnick<-c(countnick,0)
}
}
datt<-cbind(dat3[,1:4],
NickLoc = countnick,
MethLoc = countmeth,
OrientationMolecule = orientMol,
dat3[,5:ncol(dat3)],
row.names = NULL)
datt <- rbind(datt, dat4,row.names = NULL)
datf<-rbind(datf,datt,row.names = NULL)
}
'qrycmapData <- cmap
qrycontig <- as.numeric(unique(cmap$CMapId))
datf<-data.frame()
for (j in 1:length(qrycontig)){
dat3<-qrycmapData[which(qrycmapData$CMapId == qrycontig[j]),]
cntnick=0;cntmeth=0;countnick<-c();countmeth<-c()
for (hh in 1:nrow(dat3)){
if(as.numeric(dat3$LabelChannel[hh])==2){
cntnick=cntnick+1
countnick<-c(countnick,cntnick)
countmeth<-c(countmeth,0)
}else if(as.numeric(dat3$LabelChannel[hh])==1){
cntmeth=cntmeth+1
countmeth<-c(countmeth,cntmeth)
countnick<-c(countnick,0)
}else {
countmeth<-c(countmeth,0)
countnick<-c(countnick,0)
}
}
datt<-cbind(dat3[,1:4],NickLoc=countnick,MethLoc=countmeth,dat3[,5:ncol(dat3)])
datf<-rbind(datf,datt)
}'
return (datf)
}
#' Untarring the directory if needed
#'
#' @param cmaploc_mol character. Path to Bionano compressed file.
#' @return uncompressed folder with all the files for analysis
#' @examples
#' cmaploc_mol <- system.file("extdata", package="methometR")
#' untarredFolder <-untaringdirectoy(cmaploc_mol)
#' @importFrom utils untar
#' @export
untaringdirectoy <- function(cmaploc_mol){
print("Untaring directories if untarring option chosen")
untar(file.path(cmaploc_mol,"molecules.tar.gz"), exdir = cmaploc_mol)
lmolecules <- list.files(paste0(cmaploc_mol, "molecules/output/contigs/exp_refineFinal1/merged_smaps"), pattern = "*_q.cmap", full.names = TRUE)
return(lmolecules)
}
#' Mapping nick label location from contig to molecule
#'
#' @param nickrefLoc character. contig cmap data.
#' @param molcmap character. molecule cmap data.
#' @param xmapdata character. contig-molecule xmap data.
#' @param contigID character. query contig ID.
#' @param nickrefLoc character. Path to Bionano compressed file.
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @return dataframe containing the molecule file, with the nick position
#' @examples
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
#' Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
#' refxmapdat <- readingXmap(refcontigXmap)
#' refcmapdat <- readingCmap(refCmap)
#' contigcmapdat <- readingCmap(Contigqcmap)
#' nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat,
#' contigcmap = contigcmapdat, contigID = 6701,
#' returnMethod =c("dataFrame"), chrom = 4)
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' molcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' contigcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContig_r.cmap", package="methometR")
#' contigID = 6701; cntNick = 1; cntMeth=2
#' modxmap <- readingXmap(xmap)
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' modMolcmap <- modmolcmap(molcmap = modcmap,
#' xmapdata = modxmap,
#' cntNick = 1,
#' cntMeth=2)
#' contigmodcmap <- readingXmap(contigcmap)
#' modmolcmapNick <-molNickLoc(nickrefLoc = nickRef,
#' molcmap = modMolcmap,
#' xmapdata = modxmap,
#' contigID = contigID, cntNick = cntNick,
#' cntMeth = cntMeth)
#' @import utils
#' @export
molNickLoc <- function(nickrefLoc,molcmap,xmapdata, contigID, cntNick ,
cntMeth){
print("Searching for the nick labels in the molecules")
'cl <- makeCluster(5) #not to overload your computer
print(cl)
registerDoParallel(cl)'
molcmap <- molcmap
datf <- molcmap
xmapdata <- xmapdata
datFinal <- nickrefLoc
contigID = contigID
cntNick = cntNick
cntMeth = cntMeth
'print(paste("CntNick: ", cntNick))
print(paste("cntMeth: ", cntMeth))'
datFinalmol <- data.frame()
###Identifying the molecule ID
#molCmapID<-as.numeric(unique(molcmap$CMapId))
molCmapID<-as.numeric(unique(molcmap$CMapId))
#datFinalmol <- foreach (ui = 1:length(molCmapID), .combine=rbind) %dopar% {
###Extracting the site IDs of the query(moleule) and reference(contig)
for(ui in 1:length(molCmapID)){
#print(ui)
#print(paste("CmapID",molCmapID[ui]))
refloc2<-c();queryloc2<-c()
#qrycontig<-as.numeric(dat1$QryContigID)
dattt<-xmapdata[which(as.numeric(xmapdata$QryContigID) == molCmapID[ui]),]
alnt<-dattt$Alignment
refloc3<-c();queryloc2<-c()
if(length(alnt) > 1){
for(ii in length(alnt)){
stt<-strsplit(as.character(alnt[ii]),split="\\)\\(")
stt1<-as.character(stt[[1]])
for (ti in 1:length(stt1)){
if(length(grep("\\(",stt1[ti]))==1){
st2<-strsplit(stt1[ti],split="\\(")
st3<-strsplit(st2[[1]][2],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
else if(length(grep("\\)",stt1[ti]))==1){
st2<-strsplit(stt1[ti],split="\\)")
st3<-strsplit(st2[[1]][1],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
else{
st3<-strsplit(stt1[ti],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
}
}
}else{
stt<-strsplit(as.character(alnt),split="\\)\\(")
stt1<-as.character(stt[[1]])
for (ti in 1:length(stt1)){
if(length(grep("\\(",stt1[ti]))==1){
st2<-strsplit(stt1[ti],split="\\(")
st3<-strsplit(st2[[1]][2],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
else if(length(grep("\\)",stt1[ti]))==1){
st2<-strsplit(stt1[ti],split="\\)")
st3<-strsplit(st2[[1]][1],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
else{
st3<-strsplit(stt1[ti],split=",")
queryloc2<-c(queryloc2,as.numeric(st3[[1]][2]))
refloc3<-c(refloc3,as.numeric(st3[[1]][1]))
}
}
}
dattempcont <- data.frame(QueryID = queryloc2, RefID = refloc3)
###Extracting based on the refl
LocRef<-c();chrompos<-c();chromosome<-c();contigsiteID <- c()
molsiteID <- c(); contig <- c()
'datttt <- datf[which(datf$CMapId == molCmapID[ui] &
datf$LabelChannel == cntNick),]
queryloc3 <- datttt$NickLoc
unqueryloc <- unique(queryloc3)'
unqueryloc <- unique(queryloc2)
for (ll in 1:length(unqueryloc)){
#k1<-as.numeric(hash::keys(h))
#print(as.numeric(refloc2[ll]))
#val1<-as.numeric(hash::values(h,keys=as.numeric(refloc2[ll])))
datp <- dattempcont[which(dattempcont$QueryID == unqueryloc[ll]),]
val <- c()
val <- datp$RefID
#print(val)
if(length(val)> 1){
for( ql in 1:length(val)){
#val <- hash::values(ha6, keys = queryloc3[ll])
dattem<-datFinal[which(as.numeric(datFinal$CMapId) == contigID
& as.numeric(datFinal$SiteID) == val[ql]),]
#print(dim(dattem))
if(nrow(dattem) >= 1){
for(yu in 1:nrow(dattem)){
#print(paste("CMapID",cmapID[ii],sep=""))
LocRef<-c(LocRef,as.numeric(dattem$Position[yu]))
chrompos <- c(chrompos,as.numeric(dattem$chromosomePosition[yu]))
contig <- c(contig, contigID)
contigsiteID <- c(contigsiteID, dattem$SiteID[yu])
molsiteID <- c(molsiteID, unqueryloc[ll])
chromosome<-c(chromosome,as.numeric(dattem$chromosome[yu]))
}
}else{
#print(paste("CMapID",cmapID[ii],sep=""))
LocRef<-c(LocRef,0)
chrompos <- c(chrompos,NA)
contig <- c(contig, contigID)
contigsiteID <- c(contigsiteID, 0)
molsiteID <- c(molsiteID, unqueryloc[ll])
chromosome<-c(chromosome,as.numeric(dattem$chromosome[yu]))
}
}
}else{
#val <- hash::values(ha6, keys = queryloc3[ll])
dattem<-datFinal[which(as.numeric(datFinal$CMapId) == contigID
& as.numeric(datFinal$SiteID) == val),]
#print(dim(dattem))
if(nrow(dattem) >= 1){
for(yu in 1:nrow(dattem)){
#print(paste("CMapID",cmapID[ii],sep=""))
LocRef<-c(LocRef,as.numeric(dattem$Position[yu]))
chrompos <- c(chrompos,as.numeric(dattem$chromosomePosition[yu]))
contig <- c(contig, contigID)
contigsiteID <- c(contigsiteID, dattem$SiteID[yu])
molsiteID <- c(molsiteID, unqueryloc[ll])
chromosome<-c(chromosome,as.numeric(dattem$chromosome[yu]))
}
}else{
#print(paste("CMapID",cmapID[ii],sep=""))
LocRef<-c(LocRef,0)
chrompos <- c(chrompos,NA)
contig <- c(contig, contigID)
contigsiteID <- c(contigsiteID, 0)
molsiteID <- c(molsiteID, unqueryloc[ll])
chromosome<-c(chromosome,chromosome,as.numeric(dattem$chromosome[yu]))
}
}
}
datmol<-data.frame(
cmapid = rep(as.character(molCmapID[ui]),length(LocRef)),
chromosome = chromosome,
chrompos = chrompos,
LocRef=LocRef,
ContigID = contig,
ContigSiteID = contigsiteID,
MolsiteID = molsiteID)
cmapID<-unique(datmol$cmapid)
#print(cmapID)
dattemp1<-datmol[which((datmol$cmapid) == cmapID),]
datftemp<-datf[which(as.numeric(datf$CMapId) == cmapID),]
chromo = unique(datmol$chromosome)
'contigSiteID <- as.numeric(dattemp1$ContigSiteID)
Position <- (as.numeric(dattemp1$LocRef))'
molsiteID <- as.numeric(unique(dattemp1$MolsiteID))
ik = 1; ij = 0
OrientationMolecule <- as.character(unique(datftemp$OrientationMolecule))
#pnc <- paste("^", datftemp$NickLoc, "$", sep ="")
if(OrientationMolecule == "-"){
len <- nrow(datftemp)
datFinalmol_rep <- data.frame()
for(qi in nrow(datftemp):1){
#print(qi)
if(datftemp$LabelChannel[qi] == cntNick){
#dattemp3 <- datftemp[which(as.numeric((datftemp$NickLoc)[qi]) == molsiteID[ik]),]
#print(paste("molsiteID[ik]:",molsiteID[ik]))
#print(paste("ik",ik))
if(is.na(molsiteID[ik])) {
molsiteID[ik] = 0
} else{
molsiteID[ik] = molsiteID[ik]
}
if(datftemp$NickLoc[qi] == as.character(molsiteID[ik])){
dattemp2 <- dattemp1[which((dattemp1$MolsiteID) == molsiteID[ik]),]
#print(names(dattemp2))
contigSiteID <- as.numeric(dattemp2$ContigSiteID)
Position <- (as.numeric(dattemp2$LocRef))
Contig <- dattemp2$ContigID
#print(Contig)
chromPosition <- as.numeric(dattemp2$chrompos)
chromosome <- as.numeric(dattemp2$chromosome)
if(length(contigSiteID)> 1){
'print(qi)
print(OrientationMolecule)'
for(lo in 1:length(contigSiteID)){
datt<-cbind(datftemp[qi,1:4],
chromosome = chromosome[lo],
chromPosition = chromPosition[lo],
contigPosition = Position[lo],
ContigID = Contig[lo],
contigSiteID = contigSiteID[lo],
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
}
}else{
datt<-cbind(datftemp[qi,1:4],
chromosome = chromosome,
chromPosition = chromPosition,
contigPosition = Position,
ContigID = Contig,
contigSiteID = contigSiteID,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
}
ik = ik+1
}else{
#chromosome <- as.numeric(unique(dattemp2$chromosome))
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
next
}
}else if(datftemp$LabelChannel[qi] == cntMeth){
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
}else{
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol_rep<-rbind(datFinalmol_rep,datt,row.names = NULL)
}
}
datFinalmol_rep1 <-datFinalmol_rep[order(datFinalmol_rep$SiteID),]
datFinalmol <- rbind(datFinalmol, datFinalmol_rep1,row.names = NULL)
} else if(OrientationMolecule == "+"){
for(qi in 1:nrow(datftemp)){
#print(qi)
if(datftemp$LabelChannel[qi] == cntNick){
#dattemp3 <- datftemp[which(as.numeric((datftemp$NickLoc)[qi]) == molsiteID[ik]),]
#print(paste("molsiteID[ik]:",molsiteID[ik]))
#print(paste("ik",ik))
if(is.na(molsiteID[ik])) {
molsiteID[ik] = 0
} else{
molsiteID[ik] = molsiteID[ik]
}
if(datftemp$NickLoc[qi] == as.character(molsiteID[ik])){
dattemp2 <- dattemp1[which((dattemp1$MolsiteID) == molsiteID[ik]),]
#print(names(dattemp2))
contigSiteID <- as.numeric(dattemp2$ContigSiteID)
Position <- (as.numeric(dattemp2$LocRef))
Contig <- dattemp2$ContigID
#print(Contig)
chromPosition <- as.numeric(dattemp2$chrompos)
chromosome <- as.numeric(dattemp2$chromosome)
if(length(contigSiteID)> 1){
'print(1)
print(qi)
print(OrientationMolecule)'
for(lo in 1:length(contigSiteID)){
datt<-cbind(datftemp[qi,1:4],
chromosome = chromosome[lo],
chromPosition = chromPosition[lo],
contigPosition = Position[lo],
ContigID = Contig[lo],
contigSiteID = contigSiteID[lo],
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
}
}else{
'print(2)
print(qi)
print(OrientationMolecule)'
datt<-cbind(datftemp[qi,1:4],
chromosome = chromosome,
chromPosition = chromPosition,
contigPosition = Position,
ContigID = Contig,
contigSiteID = contigSiteID,
datftemp[qi,5:ncol(datftemp)],row.names = NULL)
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
}
ik = ik+1
}else{
'print(3)
print(qi)
print(OrientationMolecule)'
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)])
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
next
}
}else if(datftemp$LabelChannel[qi] == cntMeth){
'print(4)
print(qi)
print(OrientationMolecule)'
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)])
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
}else{
'print(5)
print(qi)
print(OrientationMolecule)'
datt<-cbind(datftemp[qi,1:4],
chromosome = chromo,
chromPosition = 0,
contigPosition = 0,
ContigID = unique(datmol$ContigID),
contigSiteID = 0,
datftemp[qi,5:ncol(datftemp)])
datFinalmol<-rbind(datFinalmol,datt,row.names = NULL)
}
}
}else{
print("Orientation not present")
}
}
#stopImplicitCluster(cl)
return(datFinalmol)
}
#' Mapping nick label location from contig to reference
#'
#' @param refxmap character. contig reference xmap data.
#' @param refcmap character. reference cmap data.
#' @param contigcmap character. contig cmap data.
#' @param contigID character. query contig ID.
#' @param returnMethod character. Output method. Text or dataframe.
#' @param hmdir integer. Home Directory.
#' @param chrom integer. chromosome number.
#' @return dataframe containing the molecule file, with the reference position
#' @examples
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
#' Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
#' refxmapdat <- readingXmap(refcontigXmap)
#' refcmapdat <- readingCmap(refCmap)
#' contigcmapdat <- readingCmap(Contigqcmap)
#' nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat,
#' contigcmap = contigcmapdat, contigID = 6701,
#' returnMethod =c("dataFrame"), chrom = 4)
#' @import utils
#' @import data.table
#' @export
nickReference <- function(refxmap, refcmap, contigcmap, contigID,
returnMethod =c("Text", "dataFrame"), hmdir, chrom){
print("Searching for the nick labels in the reference")
refxmap = refxmap
contigcmap <- contigcmap
contigID = contigID
chrom = chrom[1]
#print(contigID)
#print(contigID)
dat1 <- refxmap[which(refxmap$QryContigID == contigID
& refxmap$RefContigID == chrom),]
aln<-dat1$Alignment
if(length(aln) > 1){
dat <- data.frame()
for(z in 1:length(aln)){
st<-strsplit(as.character(aln[z]),split="\\)\\(")
#st1<-as.character(st[[1]])
datt <- data.frame()
for(i in 1:length(st)){
st1 <- st[[i]]
queryloc<-c(); refloc <- c()
for (ti in 1:length(st1)){
if(length(grep("\\(",st1[ti]))==1){
st2<-strsplit(st1[ti],split="\\(")
st3<-strsplit(st2[[1]][2],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
else if(length(grep("\\)",st1[ti]))==1){
st2<-strsplit(st1[ti],split="\\)")
st3<-strsplit(st2[[1]][1],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
else{
st3<-strsplit(st1[ti],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
}
queryLoc = as.numeric(queryloc)
h<-data.table(queryLoc = as.numeric(queryloc),
refLoc = as.numeric(refloc))
setkey(h, queryLoc)
#.set(h, keys=as.numeric(queryloc),values=as.numeric(refloc))
###Getting unique cmapID
contCmapID <- as.numeric(unique(dat1$QryContigID)[i])
#datFinal <- data.frame()
datFinalmol <- data.frame()
LocRef<-c();cmapid<-c();chromosome<-c(); queryref <- c(); siteID <- c()
k1 <- as.numeric(unique(queryLoc))
for (ll in 1:length(queryloc)){
if(length(grep(paste("^",as.numeric(queryloc[ll]),"$",sep=""),k1))>=1){
#print(as.numeric(queryloc[ll]))
#val1<-as.numeric(hash::values(h,keys=as.numeric(queryloc[ll])))
val1 <- h[.(as.numeric(k1[ll]))]
ref <- val1$refLoc
dattem<-refcmap[which(as.numeric(refcmap$CMapId)==chrom
& as.numeric(refcmap$SiteID) %in% ref),]
#print(dim(dattem))
LocRef<-c(LocRef,as.numeric(dattem$Position))
cmapid<-c(cmapid,as.numeric(contCmapID))
chromosome<-c(chromosome,chrom)
queryref <- c(queryref, as.numeric(queryloc[ll]))
}else{
#print(paste("CMapID",CmapID[ui],sep=""))
LocRef<-c(LocRef,0)
cmapid<-c(cmapid,as.numeric(contCmapID))
chromosome<-c(chromosome,chrom)
queryref <- c(queryref, as.numeric(queryloc[ll]))
}
}
dattemp<-data.frame(Chromosome=chromosome,cmapid=cmapid,LocRef=LocRef, queryref = queryref)
#write.table(dattemp, paste0("Contig_", unique(cmapid), "_r_mod.cmap"), row.names = FALSE)
datt <- rbind(datt, dattemp,row.names = NULL)
}
dat <- rbind(dat,datt,row.names = NULL)
}
}else{
st<-strsplit(as.character(aln),split="\\)\\(")
#st1<-as.character(st[[1]])
dat <- data.frame()
for(i in 1:length(st)){
st1 <- st[[i]]
queryloc<-c(); refloc <- c()
for (ti in 1:length(st1)){
if(length(grep("\\(",st1[ti]))==1){
st2<-strsplit(st1[ti],split="\\(")
st3<-strsplit(st2[[1]][2],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
else if(length(grep("\\)",st1[ti]))==1){
st2<-strsplit(st1[ti],split="\\)")
st3<-strsplit(st2[[1]][1],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
else{
st3<-strsplit(st1[ti],split=",")
queryloc<-c(queryloc,as.numeric(st3[[1]][2]))
refloc<-c(refloc,as.numeric(st3[[1]][1]))
}
}
'h<-hash()
.set(h, keys=as.numeric(queryloc),values=as.numeric(refloc))'
queryLoc = as.numeric(queryloc)
h<-data.table(queryLoc = as.numeric(queryloc),
refLoc = as.numeric(refloc))
setkey(h, queryLoc)
###Getting unique cmapID
contCmapID <- as.numeric(unique(dat1$QryContigID)[i])
#datFinal <- data.frame()
datFinalmol <- data.frame()
LocRef<-c();cmapid<-c();chromosome<-c(); queryref <- c(); siteID <- c()
#k1<-as.numeric(hash::keys(h))
k1 <- as.numeric(unique(h$queryLoc))
for (ll in 1:length(queryloc)){
if(length(grep(paste("^",as.numeric(queryloc[ll]),"$",sep=""),k1))>=1){
#print(as.numeric(queryloc[ll]))
val1 <- h[.(as.numeric(k1[ll]))]
ref <- val1$refLoc
dattem<-refcmap[which(as.numeric(refcmap$CMapId)==chrom
& as.numeric(refcmap$SiteID) %in% ref),]
#print(dim(dattem))
LocRef<-c(LocRef,as.numeric(dattem$Position))
cmapid<-c(cmapid,as.numeric(contCmapID))
chromosome<-c(chromosome,chrom)
queryref <- c(queryref, as.numeric(queryloc[ll]))
}else{
#print(paste("CMapID",CmapID[ui],sep=""))
LocRef<-c(LocRef,0)
cmapid<-c(cmapid,as.numeric(contCmapID))
chromosome<-c(chromosome,chrom)
queryref <- c(queryref, as.numeric(queryloc[ll]))
}
}
dattemp<-data.frame(Chromosome=chromosome,cmapid=cmapid,LocRef=LocRef, queryref = queryref)
#write.table(dattemp, paste0("Contig_", unique(cmapid), "_r_mod.cmap"), row.names = FALSE)
dat <- rbind(dat, dattemp,row.names = NULL)
}
}
####Methylation generation
cmapID<-as.numeric(unique(dat$cmapid))
datFinal <- data.frame()
#dattemp1<-dat[which(as.numeric(dat$cmapid)==cmapID),]
if(length(cmapID) > 1){
for(oo in 1:length(cmapID)){
#print(oo)
datftemp <- contigcmap[which(as.numeric(contigcmap$CMapId) == cmapID[oo]),]
#chromosome=dattemp1$Chromosome
datc <- dat[which(dat$cmapid ==cmapID[oo]),]
Position=(as.numeric(datc$LocRef))
qry <- (as.numeric(datc$queryref))
pqry <- paste0("^", qry , "$")
for( yy in 1:nrow(datftemp)){
if(as.numeric(datftemp$LabelChannel[yy])==1){
passite <- paste0("^", datftemp$SiteID[yy], "$")
g1 <- grep(passite, pqry, fixed = TRUE)
if(length(g1) == 1){
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = Position[g1],
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
else if(length(g1) > 1){
dattt <- data.frame()
for (nn in 1:length(g1)){
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = Position[g1[nn]],
datftemp[yy,7:ncol(datftemp)])
dattt <- rbind(dattt, datt, row.names = NULL)
}
datFinal<-rbind(datFinal,dattt, row.names = NULL)
}else {
'print(paste0("Locations dont match :",
datftemp$SiteID[yy]))'
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = NA,
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
}
else if(as.numeric(datftemp$LabelChannel[yy]) == 0){
posn <- Position[yy-1]
pos <- posn + (datftemp$Position[yy]-datftemp$Position[yy-1])
datt<-cbind(datftemp[yy,1:6],
chromosome=chrom,
chromosomePosition=pos,
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
else{
print("Inappropriate label")
}
}
'write.table(datFinal, file.path(hmdir, paste0("Contigs_",
cmapID[oo], "_q.cmap")),
sep = "\t",row.names = FALSE)'
}
} else if (length(cmapID) == 1){
datftemp <- contigcmap[which(as.numeric(contigcmap$CMapId)==cmapID),]
#chromosome=dattemp1$Chromosome
datc <- dat[which(dat$cmapid ==cmapID),]
Position=(as.numeric(datc$LocRef))
qry <- (as.numeric(datc$queryref))
pqry <- paste0("^", qry , "$")
for( yy in 1:nrow(datftemp)){
'print(cmapID)
print(yy)'
if(as.numeric(datftemp$LabelChannel[yy])==1){
passite <- paste0("^", datftemp$SiteID[yy], "$")
g1 <- grep(passite, pqry, fixed = TRUE)
if(length(g1) == 1){
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = Position[g1],
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
else if(length(g1) > 1){
for(pp in 1:length(g1)){
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = Position[g1[pp]],
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
}else {
#print(paste0("Locations don't match :",
# datftemp$SiteID[yy]))
datt<-cbind(datftemp[yy,1:6],
chromosome = chrom,
chromosomePosition = NA,
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
}
else if(as.numeric(datftemp$LabelChannel[yy]) == 0){
posn <- Position[yy-1]
pos <- posn + (datftemp$Position[yy]-datftemp$Position[yy-1])
datt<-cbind(datftemp[yy,1:6],
chromosome=chrom,
chromosomePosition=pos,
datftemp[yy,7:ncol(datftemp)])
datFinal<-rbind(datFinal,datt, row.names = NULL)
}
else{
print("Inappropriate label")
}
}
} else{ print("No cmap ID")}
if(returnMethod == "Text"){
write.table(datFinal, file.path(hmdir, paste0("Contigs_",
cmapID, "_q.cmap")),
sep = "\t",row.names = FALSE)
}else if(returnMethod == "dataFrame"){
return(datFinal)
}else{stop("No returnMethodSpecified")}
#return(datFinal)
}
#' Liftover of molecule methylation and nick label position to contig coordinates
#'
#' @param molcmap character. molecule cmap data.
#' @param outputType character. Output method. dataframe or text.
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @return dataframe containing the molecule file, with the reference position
#' @examples
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' modxmap <- readingXmap(xmap)
#' modMolcmap <- modmolcmap(molcmap = modcmap,
#' xmapdata = modxmap,
#' cntNick = 1,
#' cntMeth=2)
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
#' Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
#' refxmapdat <- readingXmap(refcontigXmap)
#' refcmapdat <- readingCmap(refCmap)
#' contigcmapdat <- readingCmap(Contigqcmap)
#' nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat,
#' contigcmap = contigcmapdat, contigID = 6701,
#' returnMethod =c("dataFrame"), chrom = 4)
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' molcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' contigcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContig_r.cmap", package="methometR")
#' contigID = 6701; cntNick = 1; cntMeth=2
#' contigmodcmap <- readingXmap(contigcmap)
#' modmolcmapNick <-molNickLoc(nickrefLoc = nickRef,
#' molcmap = modMolcmap,
#' xmapdata = modxmap,
#' contigID = contigID, cntNick = cntNick,
#' cntMeth = cntMeth)
#' MethylContigLoc<-molMethylLoc(molcmap = modmolcmapNick,
#' outputType = c("dataframe"),
#' cntNick = cntNick,
#' cntMeth = cntMeth)
#' @import utils
#' @export
molMethylLoc <- function(molcmap, outputType = c("dataframe", "text"), cntMeth, cntNick){
print("Searching for corresponding methylation label locations in the contig")
molcmap = molcmap
dataContig <- data.frame()
datFinalmol = molcmap
cmapID<-as.character(unique(datFinalmol$CMapId))
#print(paste("cmapID::",cmapID))
###Adding the probable location of Methylation
#datcontig<-data.frame()
'cores=detectCores()
cl <- makeCluster(5) #not to overload your computer
print(cl)
registerDoParallel(cl)'
#dataContig <- foreach(ti=1:length(cmapID), .combine=rbind) %dopar% {
for ( ti in 1:length(cmapID)){
'print(paste("ti", ti))
print(paste("cmapID", cmapID[ti]))'
datcontig<-data.frame()
datcontig<-datFinalmol[which(as.numeric(datFinalmol$CMapId) == as.numeric(cmapID[ti])),]
orientMolecule <- unique(as.character(datcontig$OrientationMolecule))
#print(orientMolecule)
datcontig[is.na(datcontig)]<-0
for( y in 1:nrow(datcontig)){
z=y-1
x=y+1
#print(paste("y", y))
if(y == 1){
if((datcontig$LabelChannel[y] == cntMeth
& datcontig$contigPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x]>0)){
if(orientMolecule == "+"){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}
else if((datcontig$LabelChannel[y]== cntMeth
& datcontig$contigPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y]== cntMeth & (datcontig$LabelChannel[x] == cntMeth & datcontig$contigPosition[x]==0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
##print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x]>0)){
if(orientMolecule == "+"){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}
else if((datcontig$LabelChannel[y]== cntNick
& datcontig$contigPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y]== cntNick
& (datcontig$LabelChannel[x] == cntMeth
& datcontig$contigPosition[x]==0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
##print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if (datcontig$LabelChannel[y] == cntNick & datcontig$contigPosition[y]>0){
datcontig$contigPosition[y] = datcontig$contigPosition[y]
}
else {
datcontig$contigPosition[y]=0
}
}
else{
if(datcontig$LabelChannel[y] == cntMeth
& (datcontig$LabelChannel[z] == cntNick
& datcontig$contigPosition[z]>0)){
'if(orientMolecule == "+"){'
'datcontig$contigLeft[y] <- as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))'
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:nrow(datcontig)]))
posn <- as.numeric(datcontig$Position[y+1:nrow(datcontig)])
contposn <- as.numeric(datcontig$contigPosition[y+1:nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (
(
(as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))/(as.numeric(posn[x]) - as.numeric(datcontig$Position[z])))* (contposn[x] - datcontig$contigPosition[z]))+ datcontig$contigPosition[z]
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
'if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}'
'} else{
datcontig$contigLeft[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[z])-as.numeric(datcontig$Position[y]))
g1<-grep(cntNick, as.character(datcontig$LabelChannel[(y+1):length(datcontig$LabelChannel)]))
posn <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x]>0 & datcontig$contigPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigRight[y] = as.numeric(contposn[x]) - (as.numeric(posn[x])-as.numeric(datcontig$Position[y]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigRight[y] = as.numeric(contposn[x]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[x]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}'
}
else if(datcontig$LabelChannel[y] == cntMeth &
(datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x]>0)){
g1<-grep(cntNick, as.character(datcontig$LabelChannel[1:z]))
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
ji= length(g1)
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(datcontig$Position[x]) - as.numeric(posn[z])))* (datcontig$contigPosition[x] - contposn[z])) + contposn[z]
ji= -1
}
else{
ji=ji-1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
'if(orientMolecule == "+"){
#datcontig$contigRight[y]=as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
} else{
datcontig$contigRight[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[y])-as.numeric(datcontig$Position[x]))
g1<-grep("1",as.character(datcontig$LabelChannel[1:z]))
ji= length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z]>0 & datcontig$contigPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigLeft[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[z]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigLeft[y] = as.numeric(contposn[z]) - (as.numeric(posn[z])-as.numeric(datcontig$Position[y]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji = -1
}
else{
ji=ji - 1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}
'
}
else if(datcontig$LabelChannel[y] == cntMeth
& ((datcontig$LabelChannel[z] == cntNick
| datcontig$LabelChannel[x] == cntNick)
& (datcontig$contigPosition[z] == 0
|datcontig$contigPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
#print(ji)
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$contigPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{
datcontig$contigPosition[y] = datcontig$contigPosition[y]
}
} else if((datcontig$contigPosition[y] == 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < contposn[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntMeth &
((datcontig$LabelChannel[z] == cntMeth
| datcontig$LabelChannel[x]== cntMeth)
& (datcontig$contigPosition[z]==0
|datcontig$contigPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$contigPosition[y]=0
ji = ji-1
# print(paste("2:",ji))
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else if((datcontig$contigPosition[y] == 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < contposn[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
} else if(datcontig$LabelChannel[y] == cntNick
& ((datcontig$LabelChannel[z] == cntNick
| datcontig$LabelChannel[x] == cntNick)
& (datcontig$contigPosition[z] == 0
|datcontig$contigPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$contigPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{
datcontig$contigPosition[y] = datcontig$contigPosition[y]
}
} else if((datcontig$contigPosition[y] == 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < contposn[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[z] == cntNick
& datcontig$contigPosition[z]>0)){
'if(orientMolecule == "+"){'
'datcontig$contigLeft[y] <- as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))'
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:nrow(datcontig)]))
posn <- as.numeric(datcontig$Position[y+1:nrow(datcontig)])
contposn <- as.numeric(datcontig$contigPosition[y+1:nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (
(
(as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))/(as.numeric(posn[x]) - as.numeric(datcontig$Position[z])))* (contposn[x] - datcontig$contigPosition[z]))+ datcontig$contigPosition[z]
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
'if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}'
'} else{
datcontig$contigLeft[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[z])-as.numeric(datcontig$Position[y]))
g1<-grep(cntNick, as.character(datcontig$LabelChannel[(y+1):length(datcontig$LabelChannel)]))
posn <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x]>0 & datcontig$contigPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigRight[y] = as.numeric(contposn[x]) - (as.numeric(posn[x])-as.numeric(datcontig$Position[y]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigRight[y] = as.numeric(contposn[x]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[x]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}'
}
else if(datcontig$LabelChannel[y] == cntNick &
(datcontig$LabelChannel[x] == cntNick
& datcontig$contigPosition[x]>0)){
g1<-grep(cntNick, as.character(datcontig$LabelChannel[1:z]))
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
ji= length(g1)
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(datcontig$Position[x]) - as.numeric(posn[z])))* (datcontig$contigPosition[x] - contposn[z])) + contposn[z]
ji= -1
}
else{
ji=ji-1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > datcontig$contigPosition[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
'if(orientMolecule == "+"){
#datcontig$contigRight[y]=as.numeric(datcontig$contigPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
} else{
datcontig$contigRight[y] = as.numeric(datcontig$contigPosition[x]) + (as.numeric(datcontig$Position[y])-as.numeric(datcontig$Position[x]))
g1<-grep("1",as.character(datcontig$LabelChannel[1:z]))
ji= length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z]>0 & datcontig$contigPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigLeft[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[z]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigLeft[y] = as.numeric(contposn[z]) - (as.numeric(posn[z])-as.numeric(datcontig$Position[y]))
datcontig$contigPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji = -1
}
else{
ji=ji - 1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$contigPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}
'
}
else if(datcontig$LabelChannel[y] == cntNick &
((datcontig$LabelChannel[z] == cntMeth
| datcontig$LabelChannel[x]== cntMeth)
& (datcontig$contigPosition[z]==0
|datcontig$contigPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))){
datcontig$contigPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < datcontig$contigPosition[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(datcontig$contigPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$contigPosition[y]=0
ji = ji-1
# print(paste("2:",ji))
}
}
if(datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else if((datcontig$contigPosition[y] == 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$contigPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$contigPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$contigPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] > contposn1[x]
| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$contigPosition[y]== 0
| is.nan(datcontig$contigPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$contigPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$contigPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < contposn[z]| datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
} else{
datcontig$contigPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$contigPosition[y] < 0){
datcontig$contigPosition[y] = 0
}else{datcontig$contigPosition[y] = datcontig$contigPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}else if (datcontig$LabelChannel[y] == cntNick & datcontig$contigPosition[y]>0){
datcontig$contigPosition[y]=datcontig$contigPosition[y]
}else{
datcontig$contigPosition[y]=0
}
}
if(datcontig$contigPosition[y] == 0
& datcontig$LabelChannel[y] == 2){
#print(paste("CMapID", cmapID[ti], "y:", y, sep = ""))
'print(y)
print(datcontig$contigPosition[y])'
}else{
}
}
dataContig<-rbind(dataContig,datcontig,row.names = NULL)
}
#stopImplicitCluster(cl)
'if(outputType == "text"){
fname=paste("Contig_",contigID[ii],"MethPositions.txt",sep="")
#rownames(datacontig)<-NULL
print(file.path(hmdir,fname,fsep=""))
write.table(dataContig,file.path(hmdir,fname,fsep="/"),row.names=FALSE)
}
else{return(dataContig)}'
return(dataContig)
}
#' Liftover of molecule methylation and nick contig position to reference coordinates
#'
#' @param molcmap character. molecule cmap data.
#' @param outputType character. Output method. dataframe or text.
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @return dataframe containing the methyl label positions mapped to the reference.
#' @examples
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' modcmap <- readingCmap(cmap)
#' modxmap <- readingXmap(xmap)
#' modMolcmap <- modmolcmap(molcmap = modcmap,
#' xmapdata = modxmap,
#' cntNick = 1,
#' cntMeth=2)
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
#' Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
#' refxmapdat <- readingXmap(refcontigXmap)
#' refcmapdat <- readingCmap(refCmap)
#' contigcmapdat <- readingCmap(Contigqcmap)
#' nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat,
#' contigcmap = contigcmapdat, contigID = 6701,
#' returnMethod =c("dataFrame"), chrom = 4)
#' xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
#' molcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
#' contigcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContig_r.cmap", package="methometR")
#' contigID = 6701; cntNick = 1; cntMeth=2
#' contigmodcmap <- readingXmap(contigcmap)
#' modmolcmapNick <-molNickLoc(nickrefLoc = nickRef,
#' molcmap = modMolcmap,
#' xmapdata = modxmap,
#' contigID = contigID, cntNick = cntNick,
#' cntMeth = cntMeth)
#' MethylRefLoc<-molMethylRefLoc(molcmap = modmolcmapNick,
#' outputType = c("dataframe"),
#' cntNick = cntNick,
#' cntMeth = cntMeth)
#' @import utils
#' @export
molMethylRefLoc <- function(molcmap, outputType = c("dataframe", "text"), cntMeth = 1, cntNick = 2){
print("Searching for the methylation label locations in the reference")
molcmap = molcmap
#molcmap = molcmapFinal
dataContig <- data.frame()
datFinalmol = molcmap
cmapID<-as.character(unique(datFinalmol$CMapId))
#print(paste("cmapID::",cmapID))
###Adding the probable location of Methylation
#datcontig<-data.frame()
'cores=detectCores()
cl <- makeCluster(5) #not to overload your computer
print(cl)
registerDoParallel(cl)'
#dataContig <- foreach(ti=1:length(cmapID), .combine=rbind) %dopar% {
for ( ti in 1:length(cmapID)){
#print(paste("ti", ti))
datcontig<-data.frame()
#datcontig<-datFinalmol[which(as.numeric(datFinalmol$CMapId)== cmapID[ti]),]
datcontig<-datFinalmol[which(as.numeric(datFinalmol$CMapId)== as.numeric(cmapID[ti])),]
orientMolecule <- unique(as.character(datcontig$OrientationMolecule))
#print(orientMolecule)
datcontig[is.na(datcontig)]<-0
for( y in 1:nrow(datcontig)){
z=y-1
x=y+1
#print(paste("y", y))
if(y == 1){
if(datcontig$LabelChannel[y] == cntMeth
& (datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x]>0)){
if(orientMolecule == "+"){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}
else if((datcontig$LabelChannel[y]== cntMeth
& datcontig$chromPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y]== cntMeth
& (datcontig$LabelChannel[x] == cntMeth
& datcontig$chromPosition[x]==0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x]>0)){
if(orientMolecule == "+"){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}
else if((datcontig$LabelChannel[y]== cntNick
& datcontig$chromPosition[y] == 0)
& (datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[x] == cntMeth
& datcontig$chromPosition[x] == 0)){
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
}
else if (datcontig$LabelChannel[y] == cntNick & datcontig$chromPosition[y]>0){
datcontig$chromPosition[y] = datcontig$chromPosition[y]
}
else {
datcontig$chromPosition[y]=0
}
}
else{
if(datcontig$LabelChannel[y] == cntMeth
& (datcontig$LabelChannel[z] == cntNick
& datcontig$chromPosition[z]>0)){
'if(orientMolecule == "+"){'
'datcontig$contigLeft[y] <- as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))'
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:nrow(datcontig)]))
posn <- as.numeric(datcontig$Position[y+1:nrow(datcontig)])
contposn <- as.numeric(datcontig$chromPosition[y+1:nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (
(
(as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))/(as.numeric(posn[x]) - as.numeric(datcontig$Position[z])))* (contposn[x] - datcontig$chromPosition[z]))+ datcontig$chromPosition[z]
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
'if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}'
'} else{
datcontig$contigLeft[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[z])-as.numeric(datcontig$Position[y]))
g1<-grep(cntNick, as.character(datcontig$LabelChannel[(y+1):length(datcontig$LabelChannel)]))
posn <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x]>0 & datcontig$chromPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigRight[y] = as.numeric(contposn[x]) - (as.numeric(posn[x])-as.numeric(datcontig$Position[y]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigRight[y] = as.numeric(contposn[x]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[x]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}'
}
else if(datcontig$LabelChannel[y] == cntMeth &
(datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x]>0)){
g1<-grep(cntNick, as.character(datcontig$LabelChannel[1:z]))
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
ji= length(g1)
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(datcontig$Position[x]) - as.numeric(posn[z])))* (datcontig$chromPosition[x] - contposn[z])) + contposn[z]
ji= -1
}
else{
ji=ji-1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
'if(orientMolecule == "+"){
#datcontig$contigRight[y]=as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
} else{
datcontig$contigRight[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[y])-as.numeric(datcontig$Position[x]))
g1<-grep("1",as.character(datcontig$LabelChannel[1:z]))
ji= length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z]>0 & datcontig$chromPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigLeft[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[z]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigLeft[y] = as.numeric(contposn[z]) - (as.numeric(posn[z])-as.numeric(datcontig$Position[y]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji = -1
}
else{
ji=ji - 1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}
'
}
else if(datcontig$LabelChannel[y] == cntMeth
& ((datcontig$LabelChannel[z] == cntNick
| datcontig$LabelChannel[x] == cntNick)
& (datcontig$chromPosition[z] == 0
|datcontig$chromPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$chromPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{
datcontig$chromPosition[y] = datcontig$chromPosition[y]
}
} else if((datcontig$chromPosition[y] == 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < contposn[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntMeth &
((datcontig$LabelChannel[z] == cntMeth
| datcontig$LabelChannel[x]== cntMeth)
& (datcontig$chromPosition[z]==0
|datcontig$chromPosition[x]==0))){g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$chromPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else if((datcontig$chromPosition[y] == 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < contposn[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntNick
& (datcontig$LabelChannel[z] == cntNick
& datcontig$chromPosition[z]>0)){
'if(orientMolecule == "+"){'
'datcontig$contigLeft[y] <- as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))'
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:nrow(datcontig)]))
posn <- as.numeric(datcontig$Position[y+1:nrow(datcontig)])
contposn <- as.numeric(datcontig$chromPosition[y+1:nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (
(
(as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))/(as.numeric(posn[x]) - as.numeric(datcontig$Position[z])))* (contposn[x] - datcontig$chromPosition[z]))+ datcontig$chromPosition[z]
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
'if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}'
'} else{
datcontig$contigLeft[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[z])-as.numeric(datcontig$Position[y]))
g1<-grep(cntNick, as.character(datcontig$LabelChannel[(y+1):length(datcontig$LabelChannel)]))
posn <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[x]>0 & datcontig$chromPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigRight[y] = as.numeric(contposn[x]) - (as.numeric(posn[x])-as.numeric(datcontig$Position[y]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigRight[y] = as.numeric(contposn[x]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[x]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji=length(g1)+1
}
else{
ji=ji+1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}'
}
else if(datcontig$LabelChannel[y] == cntNick &
(datcontig$LabelChannel[x] == cntNick
& datcontig$chromPosition[x]>0)){
g1<-grep(cntNick, as.character(datcontig$LabelChannel[1:z]))
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
ji= length(g1)
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(datcontig$Position[x]) - as.numeric(posn[z])))* (datcontig$chromPosition[x] - contposn[z])) + contposn[z]
ji= -1
}
else{
ji=ji-1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > datcontig$chromPosition[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[x]) - as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
'if(orientMolecule == "+"){
#datcontig$contigRight[y]=as.numeric(datcontig$chromPosition[x]) - (as.numeric(datcontig$Position[x])-as.numeric(datcontig$Position[y]))
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
} else{
datcontig$contigRight[y] = as.numeric(datcontig$chromPosition[x]) + (as.numeric(datcontig$Position[y])-as.numeric(datcontig$Position[x]))
g1<-grep("1",as.character(datcontig$LabelChannel[1:z]))
ji= length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
#print (paste(z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z]>0 & datcontig$chromPosition[y] == 0){
if(orientMolecule == "+"){
datcontig$contigLeft[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y])-as.numeric(posn[z]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
} else{
datcontig$contigLeft[y] = as.numeric(contposn[z]) - (as.numeric(posn[z])-as.numeric(datcontig$Position[y]))
datcontig$chromPosition[y] <- (datcontig$contigRight[y] + datcontig$contigLeft[y])/2
}
ji = -1
}
else{
ji=ji - 1
next
}
}
if(datcontig$contigRight[y] == 0 & datcontig$contigLeft[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigLeft[y]
}else if (datcontig$contigLeft[y] == 0 & datcontig$contigRight[y] > 0){
datcontig$chromPosition[y] <- datcontig$contigRight[y]
}
else if (datcontig$contigLeft[y] > 0 & datcontig$contigRight[y] > 0){
datcontig$contigLeft[y] = datcontig$contigLeft[y]
datcontig$contigRight[y] = datcontig$contigRight[y]
}
else{
datcontig$contigLeft[y] = 0; datcontig$contigRight[y] = 0;
}
}
'
}
else if(datcontig$LabelChannel[y] == cntNick
& ((datcontig$LabelChannel[z] == cntNick
| datcontig$LabelChannel[x] == cntNick)
& (datcontig$chromPosition[z] == 0
|datcontig$chromPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$chromPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{
datcontig$chromPosition[y] = datcontig$chromPosition[y]
}
} else if((datcontig$chromPosition[y] == 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
' print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < contposn[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if(datcontig$LabelChannel[y] == cntNick &
((datcontig$LabelChannel[z] == cntMeth
| datcontig$LabelChannel[x]== cntMeth)
& (datcontig$chromPosition[z]==0
|datcontig$chromPosition[x]==0))){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
g2 <- grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g1) >=1 & length(g2) >=1)){
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
#print(ji)
#print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))
if(contposn[z] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
#datcontig$contigLeft[y]=as.numeric(contposn[z]) + (as.numeric(posn[z]) - as.numeric(datcontig$Position[y]))
###Calculating x
g11<-grep(cntNick,as.character(datcontig$LabelChannel[(y+1):nrow(datcontig)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ki=1
while(ki <=length(g11)){
x1=g11[ki]
##print (paste(x1,":",y,":",cmapID[ti],":",ki,sep=""))
if(contposn1[x1] > 0
& (datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))){
datcontig$chromPosition[y] <- (((as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))/(as.numeric(posn1[x1]) - as.numeric(posn[z])))* (contposn1[x1] - contposn[z]))+ contposn[z]
ki=length(g11)+1
ji = -1
}
else{
ki=ki+1
next
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < datcontig$chromPosition[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(datcontig$chromPosition[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(datcontig$Position[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
ji = ji - 1
#print(paste("1:",ji))
}
else{
datcontig$chromPosition[y]=0
ji = ji-1
#print(paste("2:",ji))
}
}
if(datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y])){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else if((datcontig$chromPosition[y] == 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) >=1 & length(g1) == 0)){
ji=length(g1)
g1<-grep(cntNick,as.character(datcontig$LabelChannel[y+1:length(datcontig$LabelChannel)]))
posn1 <- as.numeric(datcontig$Position[(y+1):nrow(datcontig)])
contposn1 <- as.numeric(datcontig$chromPosition[(y+1):nrow(datcontig)])
ji=1
while(ji <=length(g1)){
x=g1[ji]
#print (paste(x,":",y,":",cmapID[ti],":",ji,sep=""))
if(y < x & datcontig$chromPosition[x] > 0){
if(orientMolecule == "+"){
datcontig$chromPosition[y]=as.numeric(contposn1[x]) - (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] > contposn1[x]
| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y]=as.numeric(contposn1[x]) + (as.numeric(posn1[x])-as.numeric(datcontig$Position[y]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji = ji+1
}
else{
ji=ji+1
next
}
}
} else if((datcontig$chromPosition[y]== 0
| is.nan(datcontig$chromPosition[y]))
& (length(g2) == 0 & length(g1) >= 1)){
g1 <- grep(cntNick,as.character(datcontig$LabelChannel[1:z]))
ji=length(g1)
posn <- as.numeric(datcontig$Position[1:z])
contposn <- as.numeric(datcontig$chromPosition[1:z])
while(ji > 0){
z=g1[ji]
'print(ji)
print (paste("V:",z,":",y,":",cmapID[ti],":",ji,sep=""))'
if(y > z & (contposn[z] > 0 & !is.na(contposn[z]))){
if((orientMolecule == "+")){
datcontig$chromPosition[y] = as.numeric(contposn[z]) + (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < contposn[z]| datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
} else{
datcontig$chromPosition[y] = as.numeric(contposn[z]) - (as.numeric(datcontig$Position[y]) - as.numeric(posn[z]))
if(datcontig$chromPosition[y] < 0){
datcontig$chromPosition[y] = 0
}else{datcontig$chromPosition[y] = datcontig$chromPosition[y]}
}
ji= ji - 1
} else{
ji = ji - 1
next
}
}
}else{
#print("Locations do not match!!!!!")
}
}
else if (datcontig$LabelChannel[y] == cntNick & datcontig$chromPosition[y]>0){
datcontig$chromPosition[y]=datcontig$chromPosition[y]
}
else{
datcontig$chromPosition[y]=0
}
}
}
dataContig<-rbind(dataContig,datcontig,row.names = NULL)
}
#stopImplicitCluster(cl)
'if(outputType == "text"){
fname=paste("Contig_",contigID[ii],"MethPositions.txt",sep="")
#rownames(datacontig)<-NULL
print(file.path(hmdir,fname,fsep=""))
write.table(dataContig,file.path(hmdir,fname,fsep="/"),row.names=FALSE)
}
else{return(dataContig)}'
return(dataContig)
}
#' Extracting contig information
#'
#' @param contigRefxmap character. Contig xmap data.
#' @param chrom character. Chromosome of interest.
#' @param startPos integer.Start position.
#' @param endPos integer. End position.
#' @return dataframe with data extracted from xmap.
#' @examples
#' refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
#' modxmap <- readingXmap(refcontigXmap)
#' extractedInfo<-contigextract(contigRefxmap = modxmap, chrom = 4, startPos = 100000, endPos = 200000)
#' @import utils
#' @export
contigextract <- function(contigRefxmap, chrom, startPos, endPos){
print("Extracting Contig information")
if(startPos > 0 & endPos > 0 & chrom >0){
dat1 <- contigRefxmap[which(contigRefxmap$RefStartPos <= startPos
& contigRefxmap$RefEndPos >= endPos
& contigRefxmap$RefContigID == chrom ),]
}else if(startPos > 0 & endPos == 0 & chrom >0){
dat1 <- contigRefxmap[which(contigRefxmap$RefStartPos <= startPos
& contigRefxmap$RefEndPos >= startPos
& contigRefxmap$RefContigID == chrom ),]
}else if(startPos == 0 & endPos == 0 & chrom >0){
dat1 <- contigRefxmap[which(contigRefxmap$RefContigID == chrom ),]
}else{
print("chromosome or start or end information required!!")
}
contigID <- dat1$QryContigID
chrom <- unique(dat1$RefContigID)
dat <- data.frame(contigID = contigID, chrom = rep(chrom, length(contigID)))
return(dat)
}
#' Main function to call the extraction, modification and quantification process.
#'
#' @param cmaploc_mol character. path to the cmap folder.
#' @param untar boolean. untar option. True or False/
#' @param cntNick integer. Nick label value.
#' @param cntMeth integer. Meth label value.
#' @param selectedRegion boolean. if TRUE, selected region is analyzed and
#' the user provides chromosome and start and end point. If FALSE, whole
#' genome analysed.
#' @param chrom character. Chromosome number if selectedRegion is TRUE
#' @param startPos integer. Start of the query if selectedRegion is TRUE
#' @param endPos integer. End of the query if selectedRegion is TRUE
#' @param outputFormat Character. Choices are individualText, multipleText and
#' dataframe.
#' @param path Character. Path of the folder where log files needs to be written
#' to.
#' @param logFilename character. Log file name.
#' @return dataframe or text files containing the modified files.
#' @examples
#'\dontrun{
#' molcmap <- system.file("extdata", "SampMolecule.cmap", package="methometR")
#' cmap <- system.file("extdata", "SampContig.cmap", package="methometR")
#' bed<-molMethylRefLoc(nickrefLoc,molcmap,xmapdata, contigID, cntNick ,
#' cntMeth)
#'}
#' @import utils
#' @import logr
#' @export
extracting_modifying_methLabels <- function(cmaploc_mol,
untar = FALSE, cntNick, cntMeth, selectedRegion = TRUE, chrom, startPos, endPos,
outputFormat = c("individualText", "multipleText",
"dataFrame"), path, logFilename){
#logFilename = ""
logFilename = logFilename
ifelse(logFilename == "",
log_open(file.path(path, "logmethometR.txt")),
log_open(file.path(path, logFilename)))
log_print("----methometr Package----")
print("----Function to map nick and methylation label to reference----")
log_print("----Function to map nick and methylation label to reference----")
cntNick =cntNick; cntMeth = cntMeth;
untar = untar; cmaploc_mol = cmaploc_mol;
selectedRegion = selectedRegion;
outputFormat = outputFormat;
path = path
refcmap <- data.frame();
querycmap <- data.frame();contigRefxmap <- data.frame()
if(untar == TRUE){
print("---Untaring and reading molecule and contig info---")
log_print("---Untaring and reading molecule and contig info---")
untaringdirectoy(cmaploc_mol)
st <- strsplit(cmaploc_mol, split = ".zip")
cmapPath <- st[[1]][1]
##contig and reference maps
print("Extracting file paths for required contig and reference files")
contigRefpath <- file.path(cmapPath, "output/contigs/exp_refineFinal1_sv/merged_smaps/")
contRefXmappath <- list.files(contigRefpath, pattern = "*.xmap", full.names = TRUE)
Refcmappath <- list.files(contigRefpath, pattern = "*_r.cmap", full.names = TRUE)
Querycmappath <- list.files(contigRefpath, pattern = "*_q.cmap", full.names = TRUE)
print("Reading contig, molecule and reference xmap")
refcmap <- readingCmap(Refcmappath)
querycmap <- readingCmap(Querycmappath)
contigRefxmap <- readingXmap(xmap = contRefXmappath)
chrom1 <- unique(contigRefxmap$RefContigID)
##contig and molecule maps
contigMolPath <- file.path(cmapPath, "output/contigs/exp_refineFinal1/alignmol/merge/")
lmolecules <- list.files(cmaploc_mol, pattern = "*.xmap", full.names = FALSE)
st1 <- strsplit(lmolecules, split = "contig")
st2 <- sapply(st1, "[[", 2)
st3 <- strsplit(st2, split = "\\.")
contigID <- sapply(st3, "[[", 1)
lcontig <- list.files(cmaploc_mol, pattern = "*_r.cmap", full.names = TRUE)
lxmap <- list.files(cmaploc_mol, pattern = "*.", full.names = TRUE)
}
else {
print("---Reading molecule and contig info---")
log_print("---Reading molecule and contig info---")
##contig and reference maps
print("Extracting file paths for required contig and reference files")
contigRefpath <- file.path(cmaploc_mol, "output/contigs/exp_refineFinal1_sv/merged_smaps/")
contRefXmappath <- list.files(contigRefpath, pattern = "*.xmap", full.names = TRUE)
Refcmappath <- list.files(contigRefpath, pattern = "*_r.cmap", full.names = TRUE)
Querycmappath <- list.files(contigRefpath, pattern = "*_q.cmap", full.names = TRUE)
print("Reading contig, molecule and reference xmap")
refcmap <- readingCmap(Refcmappath)
querycmap <- readingCmap(Querycmappath)
contigRefxmap <- readingXmap(xmap = contRefXmappath)
chrom1 <- unique(contigRefxmap$RefContigID)
##contig and molecule maps
contigMolPath <- file.path(cmaploc_mol, "output/contigs/exp_refineFinal1/alignmol/merge")
lmolecules <- list.files(contigMolPath, pattern = "*.xmap", full.names = FALSE)
st1 <- strsplit(lmolecules, split = "contig")
st2 <- sapply(st1, "[[", 2)
st3 <- strsplit(st2, split = "\\.")
contigID <- sapply(st3, "[[", 1)
}
datmolInfo <- data.frame()
if(selectedRegion == FALSE){
modmol <- data.frame()
print("Selected region is FALSE")
'pp <- paste("Total number of contigs to be processed:", length(contigID))
log_print(pp)
print(paste("Total number of contigs to be processed:", length(contigID)))'
chrom <- sort(chrom1)
for(uu in seq_along(chrom)){
datcont <- contigRefxmap[which(contigRefxmap$RefContigID == chrom[uu]),]
contigID <- datcont$QryContigID
pa <- paste("---Processing Chromosome",
paste("chr_", chrom[uu], sep = ""),
"--", sep = "")
print(pa)
log_print(pa)
pa1 <- paste("---Number of contigs for chromosme ",
paste("chr_", chrom[uu], sep = ""), ":",
length(contigID), "---", sep = "")
#pp1 <- paste("---Number of contigs for chromosme1:", length(contigID))
print(pa1)
log_print(pa1)
if(dir.exists(file.path(path, paste("chr_", chrom[uu], sep = "")))
& length(list.files(path = file.path(path, paste("chr_", chrom[uu], sep = "")))) > 0){
pa7 <- paste("chr_", chrom[uu],": already processed", sep = "")
log_print(pa7)
next;
}else if(!dir.exists(file.path(path, paste("chr_", chrom[uu], sep = "")))){
pp2 <- paste("---Creating directory for Chromosome", chrom[uu], "--", sep = "")
print(paste("---Creating directory for Chromosome", chrom[uu], "--", sep = ""))
log_print(pp2)
dir.create(file.path(path, paste("chr_", chrom[uu], sep = "")))
outpath <- file.path(path, paste("chr_", chrom[uu], sep = ""))
}else{
outpath <- file.path(path, paste("chr_", chrom[uu], sep = ""))
}
if(length(contigID) > 1){
for (ii in seq_along(contigID)){
contigRefxmap = contigRefxmap;refcmap = refcmap
#for (ii in 803:length(contigID)){
print(paste("Contig being analyzed:", contigID[ii], sep = ""))
pp5 <- paste("Contig being analyzed:", contigID[ii], sep = "")
log_print(pp5)
print("Reading contig, molecule and reference xmap")
contigmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],"_r.cmap",sep = ""), full.names = TRUE)
molmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap",sep = ""), full.names = TRUE)
xmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],".xmap",sep = ""), full.names = TRUE)
#contigdat <- readingCmap(contigmap)
if(molmap == ""){
print(paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap", "is discarded from analysis!!!"))
pp4 <- paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap", "is discarded from analysis!!!")
log_print(pp4)
next;
}else{
moldat <- readingCmap(molmap)
}
dat1_t <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]),]
if((nrow(dat1_t) > 1)
& (length(unique(dat1_t$RefContigID)) > 1)){
message("Work in progress translocation function")
next;
}else{
dat1 <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]
& contigRefxmap$RefContigID == chrom[uu]),]
}
xmapdat <- readingXmap(xmap)
if(all(is.na((moldat[1:3,]))) == TRUE
| all(is.na((xmapdat[1:3,]))) == TRUE
| all(is.na((querycmap[1:3,]))) == TRUE){
log_print("Either xmap,molecule cmap or reference cmap file empty !!!!")
print("Either xmap,molecule cmap or reference cmap file empty !!!!")
next;
}else{moldat = moldat; xmapdat = xmapdat}
if(nrow(dat1) >= 1){
contigID[ii] = contigID[ii]
#chrom = unique(dat1$RefContigID)
#chrom2 = unique(dat1$RefContigID)
#modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
'if(length(chrom2) > 1){
nickrefLoc <- data.frame()
for(oo in 1:length(chrom2)){
nickrefLoc1 <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom2[oo],
returnMethod = "dataFrame")
nickrefLoc <- rbind(nickrefLoc, nickrefLoc1,row.names = NULL)
}
}else{
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom2,
returnMethod = "dataFrame")
}'
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom[uu],
returnMethod = "dataFrame")
modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
methylNickLoc <- molNickLoc(nickrefLoc = nickrefLoc,
molcmap = modmolCmapdat,
xmapdata = xmapdat,
contigID = contigID[ii],
cntNick = cntNick,
cntMeth = cntMeth)
molcmapFinal <- molMethylLoc(methylNickLoc, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
molcmapFinal1 <- molMethylRefLoc(molcmapFinal, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
print (outpath)
if(outputFormat == "individualText"){
write.table(molcmapFinal1, file.path(outpath, paste("modifiedMol_", contigID[ii], ".txt", sep = "")))
}else if(outputFormat == "dataFrame"){
modmol <- rbind(modmol,molcmapFinal1, row.names = NULL)
}else if(outputFormat == "multipleText"){
modmol <- rbind(modmol,molcmapFinal1, row.names = NULL)
print("Will print outside the loop")
}else{stop("outputMethod Incorrect!!!!")}
}else{ print(paste("Contig:", contigID[ii], " is absent."))
next;}
}
}else{
chrom = chrom1
datcont <- contigRefxmap[which(contigRefxmap$RefContigID == chrom),]
contigID <- datcont$QryContigID
pa <- paste("---Processing Chromosome",
paste("chr_", chrom, sep = ""),
"--", sep = "")
print(pa)
log_print(pa)
pa1 <- paste("---Number of contigs for chromosme ",
paste("chr_", chrom, sep = ""), ":",
length(contigID), "---", sep = "")
#pp1 <- paste("---Number of contigs for chromosme1:", length(contigID))
print(pa1)
log_print(pa1)
pp6 <- (paste("Contig being analyzed:", contigID, sep = ""))
print(pp6)
log_print(pp6)
if(dir.exists(file.path(path, paste("chr_", chrom, sep = "")))
& length(list.files(path = file.path(path, paste("chr_", chrom, sep = "")))) > 0){
pa7 <- paste("chr_", chrom,": alreay processed", sep = "")
log_print(pa7)
next;
}else if(!dir.exists(file.path(path, paste("chr_", chrom, sep = "")))){
pp2 <- paste("---Creating directory for Chromosome", chrom, "--", sep = "")
print(paste("---Creating directory for Chromosome", chrom, "--", sep = ""))
log_print(pp2)
dir.create(file.path(path, paste("chr_", chrom, sep = "")))
outpath <- file.path(path, paste("chr_", chrom, sep = ""))
}else{
outpath <- file.path(path, paste("chr_", chrom, sep = ""))
}
'dat1 <- refxmap[which(refxmap$QryContigID == contigID),]
chrom = unique(dat1$RefContigID)'
contigmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,"_r.cmap",sep = ""), full.names = TRUE)
molmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,"_q.cmap",sep = ""), full.names = TRUE)
xmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,".xmap",sep = ""), full.names = TRUE)
#contigdat <- readingCmap(contigmap)
if(molmap == NA){
print(paste("exp_refineFinal1_contig",contigID,"_q.cmap", "is discarded from analysis!!!"))
pp4 <- paste("exp_refineFinal1_contig",contigID,"_q.cmap", "is discarded from analysis!!!")
log_print(pp4)
next;
}else{
moldat <- readingCmap(molmap)
}
xmapdat <- readingXmap(xmap = xmap)
if(is.na(moldat) == TRUE
| is.na(xmapdat) == TRUE){
log_print("Either xmap,molecule cmap or reference cmap file empty !!!!")
print("Either xmap,molecule cmap or reference cmap file empty !!!!")
next;
}else{moldat = moldat; xmapdat = xmapdat}
#dat1 <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]),]
if(nrow(dat1) >= 1){
contigID = contigID
#chrom = unique(dat1$RefContigID)
chrom2 = unique(dat1$RefContigID)
xmapdat <- readingXmap(xmap)
#modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
if(length(chrom2) > 1){
nickrefLoc <- data.frame()
for(oo in 1:length(chrom2)){
nickrefLoc1 <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID,
chrom = chrom2[oo],
returnMethod = "dataFrame")
nickrefLoc <- rbind(nickrefLoc, nickrefLoc1,row.names = NULL)
}
}else{
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID,
chrom = chrom2,
returnMethod = "dataFrame")
}
modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
methylNickLoc <- molNickLoc(nickrefLoc = nickrefLoc,
molcmap = modmolCmapdat,
xmapdata = xmapdat,
contigID = contigID,
cntNick = cntNick,
cntMeth = cntMeth)
molcmapFinal <- molMethylLoc(methylNickLoc, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
molcmapFinal1 <- molMethylRefLoc(molcmapFinal, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
print (outpath)
if(outputFormat == "individualText"){
write.table(molcmapFinal1, file.path(outpath, paste("modifiedMol_", contigID, ".txt", sep = "")))
}else if(outputFormat == "dataFrame"){
modmol <- rbind(modmol,molcmapFinal1,row.names = NULL)
}else if(outputFormat == "multipleText"){
modmol <- rbind(modmol,molcmapFinal1,row.names = NULL)
print("Will print outside the loop")
}else{stop("outputMethod Incorrect!!!!")}
}else{ print(paste("Contig:", contigID, " is absent."))
next;}
}
if(outputFormat == "multipleText"){
if(length(unique(modmol$ContigID)) > 1){
contig <- unique(modmol$ContigID)
contigname <- paste(contig, collapse = "_")
write.table(modmol, file.path(outpath, paste("modifiedMol_", contigname, ".txt", sep = "")))
}else if (length(unique(modmol$ContigID)) == 1){
print("Individual contig files have been written !!")
}else{stop("No contigs found !!!")}
}else if(outputFormat == "individualText"){
log_print("Individual contig files have already been written !!")
}else if(outputFormat == "dataFrame"){
return(modmol)
}else{stop("outputMethod Incorrect!!!!")}
pp6 <- paste("---Finished Processing", chrom[uu], "--", sep = "")
log_print(pp6)
}
}else if(selectedRegion == TRUE){
print("Selected region is TRUE")
dir.create(file.path(path, "Selected"))
chrom = chrom;
startPos = startPos; endPos = endPos;
dat1 <- contigextract(contigRefxmap = contigRefxmap,
chrom = chrom, startPos = startPos, endPos = endPos)
if(nrow(dat1) >= 1){
contigID <- dat1$contigID
chrom <- unique(dat1$chrom)
}else{stop("Selected region does not have a contig mapped to it!!!")}
print(paste("Total number of contigs to be processed:", length(contigID)))
'pp7 <- paste("---Creating directory for Chromosome", chrom, "--", sep = "")
print(paste("---Creating directory for Chromosome", chrom, "--", sep = ""))
outpath <- dir.create(file.path(path, paste("chr_", chrom[uu], sep = "")))'
if(dir.exists(file.path(path, "Selected", paste("chr_", chrom, sep = "")))
& length(list.files(path = file.path(path, paste("chr_", "Selected", chrom, sep = "")))) > 0){
pa7 <- paste("chr_", chrom,": alreay processed", sep = "")
log_print(pa7)
}else if(!dir.exists(file.path(path, "Selected", paste("chr_", chrom, sep = "")))){
pp2 <- paste("---Creating directory for Chromosome", chrom, "--", sep = "")
print(paste("---Creating directory for Chromosome", chrom, "--", sep = ""))
log_print(pp2)
dir.create(file.path(path, "Selected", paste("chr_", chrom, sep = "")))
outpath <- file.path(path, "Selected", paste("chr_", chrom, sep = ""))
}else{
outpath <- file.path(path, "Selected", paste("chr_", chrom, sep = ""))
}
if(length(contigID) > 1){
print(nrow(contigRefxmap));
print(nrow(refcmap));
for (ii in 1:length(contigID)){
#for (ii in 803:length(contigID)){
print(paste("Contig being analyzed:", contigID[ii], sep = ""))
pp5 <- paste("Contig being analyzed:", contigID[ii], sep = "")
log_print(pp5)
print("Reading contig, molecule and reference xmap")
contigmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],"_r.cmap",sep = ""), full.names = TRUE)
molmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap",sep = ""), full.names = TRUE)
xmap <- list.files (contigMolPath, pattern = paste("exp_refineFinal1_contig",contigID[ii],".xmap",sep = ""), full.names = TRUE)
#contigdat <- readingCmap(contigmap)
if(molmap == ""){
print(paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap", "is discarded from analysis!!!"))
pp4 <- paste("exp_refineFinal1_contig",contigID[ii],"_q.cmap", "is discarded from analysis!!!")
log_print(pp4)
next;
}else{
moldat <- readingCmap(molmap)
}
dat1 <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]),]
xmapdat <- readingXmap(xmap)
if(all(is.na((moldat[1:3,]))) == TRUE
| all(is.na((xmapdat[1:3,]))) == TRUE
| all(is.na((querycmap[1:3,]))) == TRUE){
log_print("Either xmap,molecule cmap or reference cmap file empty !!!!")
print("Either xmap,molecule cmap or reference cmap file empty !!!!")
next;
}else{moldat = moldat; xmapdat = xmapdat}
if(nrow(dat1) >= 1){
contigID[ii] = contigID[ii]
#chrom = unique(dat1$RefContigID)
chrom2 = unique(dat1$RefContigID)
#modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
if(length(chrom2) > 1){
nickrefLoc <- data.frame()
for(oo in 1:length(chrom2)){
nickrefLoc1 <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom2[oo],
returnMethod = "dataFrame")
nickrefLoc <- rbind(nickrefLoc, nickrefLoc1,row.names = NULL)
}
}else{
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID[ii],
chrom = chrom2,
returnMethod = "dataFrame")
}
modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
methylNickLoc <- molNickLoc(nickrefLoc = nickrefLoc,
molcmap = modmolCmapdat,
xmapdata = xmapdat,
contigID = contigID[ii],
cntNick = cntNick,
cntMeth = cntMeth)
molcmapFinal <- molMethylLoc(methylNickLoc, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
molcmapFinal1 <- molMethylRefLoc(molcmapFinal, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
if(outputFormat == "individualText"){
write.table(molcmapFinal1, file.path(outpath, paste("modifiedMol_", contigID[ii], ".txt", sep = "")))
}else if(outputFormat == "dataFrame"){
modmol <- rbind(modmol,molcmapFinal1, row.names = NULL)
}else if(outputFormat == "multipleText"){
modmol <- rbind(modmol,molcmapFinal1, row.names = NULL)
print("Will print outside the loop")
}else{stop("outputMethod Incorrect!!!!")}
}else{ print(paste("Contig:", contigID[ii], " is absent."))
next;}
}
}else{
print(paste("Contig being analyzed:", contigID, sep = ""))
'dat1 <- refxmap[which(refxmap$QryContigID == contigID),]
chrom = unique(dat1$RefContigID)'
contigmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,"_r.cmap",sep = ""), full.names = TRUE)
molmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,"_q.cmap",sep = ""), full.names = TRUE)
xmap <- list.files (cmaploc_mol, pattern = paste("exp_refineFinal1_contig",contigID,".xmap",sep = ""), full.names = TRUE)
#contigdat <- readingCmap(contigmap)
if(molmap == NA){
print(paste("exp_refineFinal1_contig",contigID,"_q.cmap", "is discarded from analysis!!!"))
pp4 <- paste("exp_refineFinal1_contig",contigID,"_q.cmap", "is discarded from analysis!!!")
log_print(pp4)
}else{
moldat <- readingCmap(molmap)
}
xmapdat <- readingXmap(xmap = xmap)
if(is.na(moldat) == TRUE
| is.na(xmapdat) == TRUE){
log_print("Either xmap,molecule cmap or reference cmap file empty !!!!")
print("Either xmap,molecule cmap or reference cmap file empty !!!!")
}else{moldat = moldat; xmapdat = xmapdat}
#dat1 <- contigRefxmap[which(contigRefxmap$QryContigID == contigID[ii]),]
if(nrow(dat1) >= 1){
contigID = contigID
#chrom = unique(dat1$RefContigID)
chrom2 = unique(dat1$RefContigID)
xmapdat <- readingXmap(xmap)
#modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
if(length(chrom2) > 1){
nickrefLoc <- data.frame()
for(oo in 1:length(chrom2)){
nickrefLoc1 <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID,
chrom = chrom2[oo],
returnMethod = "dataFrame")
nickrefLoc <- rbind(nickrefLoc, nickrefLoc1,row.names = NULL)
}
}else{
nickrefLoc <- nickReference(refxmap = contigRefxmap,
refcmap = refcmap,
contigcmap = querycmap,
contigID = contigID,
chrom = chrom2,
returnMethod = "dataFrame")
}
modmolCmapdat <- modmolcmap(molcmap = moldat, xmapdata = xmapdat, cntNick = cntNick, cntMeth = cntMeth)
methylNickLoc <- molNickLoc(nickrefLoc = nickrefLoc,
molcmap = modmolCmapdat,
xmapdata = xmapdat,
contigID = contigID,
cntNick = cntNick,
cntMeth = cntMeth)
molcmapFinal <- molMethylLoc(methylNickLoc, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
molcmapFinal1 <- molMethylRefLoc(molcmapFinal, cntNick = cntNick, cntMeth = cntMeth, outputType = c("dataframe"))
if(outputFormat == "individualText"){
write.table(molcmapFinal1, file.path(outpath, paste("modifiedMol_", contigID, ".txt", sep = "")))
}else if(outputFormat == "dataFrame"){
modmol <- rbind(modmol,molcmapFinal1,row.names = NULL)
}else if(outputFormat == "multipleText"){
modmol <- rbind(modmol,molcmapFinal1,row.names = NULL)
print("Will print outside the loop")
}else{stop("outputMethod Incorrect!!!!")}
}else{ print(paste("Contig:", contigID, " is absent."))
}
}
if(outputFormat == "multipleText"){
if(length(unique(modmol$ContigID)) > 1){
contig <- unique(modmol$ContigID)
contigname <- paste(contig, collapse = "_")
write.table(modmol, file.path(outpath, paste("modifiedMol_", contigname, ".txt", sep = "")))
}else if (length(unique(modmol$ContigID)) == 1){
print("Individual contig files have been written !!")
}else{stop("No contigs found !!!")}
}else if(outputFormat == "individualText"){
log_print("Individual contig files have already been written !!")
}else if(outputFormat == "dataFrame"){
return(modmol)
}else{stop("outputMethod Incorrect!!!!")}
pp10 <- paste("---Finished Processing Selected Region---")
log_print(pp10)
}else{stop("Selected Region Not Selected!!!")}
log_print("Molecule cmaps modified !!!")
print("Molecule cmaps modified !!!")
log_print("---Closing Log Files!!!---")
log_close()
#return(paste("query methylation Labels Modified"))
#return (fname1)
}
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