R/filterread_Trio_SVMerge.r
In VilainLab/Nanotator: Next generation structural variant annotation and classification
Defines functions
run_bionano_filter_SVMerge_Trio
Documented in
run_bionano_filter_SVMerge_Trio
#' Getting the data from annotated smaps to extract SV
#' information based on type of variants.
#'
#' @param input_fmt_geneList character. Choice of gene list input
#' Text or Dataframe.
#' @param input_fmt_SV character. Choice of gene list input
#' Text or Dataframe.
#' @param smap character. SV file name.
#' @param svData Dataframe Input data containing SV data.
#' @param dat_geneList Dataframe Input data containing geneList data.
#' @param fileName Character Name of file containing Gene List data.
#' @param outpath Character Directory to the output file.
#' @param outputFilename Character Output filename.
#' @param RZIPpath Character Path for the Rtools Zip package.
#' @param outputType Character. Variants in excel tabs or in different csv files.
#' Options Excel or csv.
#' @param EnzymeType Character. Enzyme type used. Options SVMerge or SE.
#' @param fileprefix Character. fileprefix to use for each of the files in the directory.
#' @param directoryName Character. Directory name where individual SV files will be stored.
#' @param primaryGenesPresent boolean Checks whether the primary gene List is present or not.
#' @return Excel file containing the annotated SV map, tabs divided based on
#' type of SVs.
#' @examples
#' \dontrun{
#' smapName <- "GM24385_DLE-1_P_trio_hg19.smap"
#' outputFilename <- "GM24385_DLE-1_P_trio_hg19_out"
#' smappath <- system.file("extdata", smapName, package = "nanotatoR")
#' outpath <- system.file("extdata", smapName, package = "nanotatoR")
#' RZIPpath <- system.file("extdata", "zip.exe", package = "nanotatoR")
#' run_bionano_filter_SVMerge_Trio (input_fmt_geneList = c("Text"),
#' input_fmt_SV = c("Text"),
#' smap = smappath,
#' dat_geneList = dat_geneList,
#' RZIPpath = RZIPpath, EnzymeType = c("SVMerge"),
#' outputType = c("Excel"),
#' primaryGenesPresent = FALSE,
#' outputFilename = outputFilename,
#' outpath = outpath)#' }
#' @import openxlsx
#' @import hash
#' @importFrom stats na.omit
#' @export
run_bionano_filter_SVMerge_Trio <- function(
input_fmt_geneList = c("Text", "dataFrame"),
input_fmt_SV = c("Text", "dataFrame"),
EnzymeType = c("SVMerge", "SE"),
smap = NULL, svData, dat_geneList, fileName, outpath,
outputFilename = "", RZIPpath, primaryGenesPresent = TRUE,
outputType = c("Excel", "csv"), directoryName, fileprefix) {
# library(openxlsx)
# library(hash)
# setwd(path)##change the directory to your working directory
Sys.setenv("R_ZIPCMD" = RZIPpath)
## GeneList Input Format
ha <- hash()
# ll<-list.files(pattern="txt")
if(input_fmt_SV=="dataFrame"){
smapdata = svData
if(EnzymeType == "SVMerge"){
#smapdata <- readSMap(smap, input_fmt_smap = "Text")
SVID<-smapdata$SVIndex
}
else{
#smapdata <- readSMap_DLE(smap, input_fmt_smap)
SVID<-smapdata$SmapEntryID
}
}
else if(input_fmt_SV=="Text"){
if(EnzymeType == "SVMerge"){
smapdata <- readSMap(smap, input_fmt_smap = "Text")
SVID<-smapdata$SVIndex
}
else{
smapdata <- readSMap_DLE(smap, input_fmt_smap = "Text")
SVID<-smapdata$SmapEntryID
}
}
else{
stop("Input format for SMAP Incorrect")
}
r <- smapdata
primaryGenesPresent = primaryGenesPresent
if (primaryGenesPresent == TRUE){
if (input_fmt_geneList == "Text") {
rr <- read.table(fileName, header = TRUE)
}
else if (input_fmt_geneList == "dataFrame") {
rr <- dat_geneList
}
else {
stop("input_fmt_geneList Incorrect!!")
}
ogene <- as.character(r$OverlapGenes_strand_perc)
upgene <- as.character(r$Upstream_nonOverlapGenes_dist_kb)
dngene <- as.character(r$Downstream_nonOverlapGenes_dist_kb)
# nogene<-c(upgene,dngene)
### OverlapGene
dataPGOV <- overlappingGenes (rr, ogene)
### Non-Overlap Up-stream Gene
dataPGUP <- nonOverlappingUPGenes (rr, upgene)
### Non-Overlap Down-stream Gene
dataPGDN <- nonOverlappingDNGenes (rr, dngene)
### Non-OverlapDnGene
# len<-length(pagene)-length(pg)
# genesPG<-c(as.character(pg),rep("-",len))
data <- data.frame(cbind(
r, Overlap_PG = as.character(dataPGOV$pagene),
Overlap_Terms = as.character(dataPGOV$pagene_term),
Overlap_ClinicalSig = as.character(dataPGOV$pagene_clinSig),
Non_Overlap_UP_PG = as.character(dataPGUP$nopageneup),
Non_Overlap_UP_Terms = as.character(dataPGUP$nopageneup_term),
Non_Overlap_UP_ClinicalSig = as.character(
dataPGUP$nopageneup_clinSig),
Non_Overlap_DN_PG = as.character(dataPGDN$nopagenedn),
Non_Overlap_DN_Terms = as.character(dataPGDN$nopagenedn_term),
Non_Overlap_DN_ClinicalSig = as.character(
dataPGDN$nopagenedn_clinSig)))
}else if (primaryGenesPresent == FALSE){
data <- smapdata
}else {stop("primaryGenesPresent Incorrect!!")}
##
data$BNG_Freq_Perc_Filtered<-gsub("-", 0, as.character(
data$BNG_Freq_Perc_Filtered))
data$BNG_Freq_Perc_UnFiltered<-gsub("-",0,as.character(
data$BNG_Freq_Perc_UnFiltered))
data$DGV_Freq_Perc<-as.numeric(data$DGV_Freq_Perc)
data$Internal_Freq_Perc_Filtered<-as.numeric(
data$Internal_Freq_Perc_Filtered)
data$Internal_Freq_Perc_Unfiltered<-as.numeric(
data$Internal_Freq_Perc_Unfiltered)
data$BNG_Freq_Perc_Filtered<-as.numeric(data$BNG_Freq_Perc_Filtered)
data$BNG_Freq_Perc_UnFiltered<-as.numeric(data$BNG_Freq_Perc_UnFiltered)
data$DECIPHER_Frequency<-as.numeric(data$DECIPHER_Frequency)
data$Type1<-as.character(data$Type1)
data$Type2<-as.character(data$Type2)
dat <- data[which(data$Type %in% "insertion"), ]
dat1 <- data[which(data$Type %in% "deletion"), ]
dat44 <- data[which(data$Type %in% "duplication"), ]
dat45 <- data[which(data$Type %in% "duplication_split"), ]
dat46 <- data[which(data$Type %in% "duplication_inverted"), ]
dat_dup_rem<-rbind(dat44,dat45,dat46)
dat_dup_rem_FINAL<-dat_dup_rem[which(((
dat_dup_rem$Type %in% "duplication")
| (dat_dup_rem$Type %in% "duplication_split")
| (dat_dup_rem$Type %in% "duplication_inverted"))
& (((dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "fail"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "-"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass")))), ]
dat3 <- rbind(dat1, dat, dat_dup_rem_FINAL)
dat10 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-")
| (dat3$Found_in_self_BSPQI_molecules == "-"
& dat3$Found_in_self_BSSSI_molecules == "yes"))
& ((dat3$Found_in_parents_BSPQI_molecules == "none"
& dat3$Found_in_parents_BSSSI_molecules == "none")
| (dat3$Found_in_parents_BSPQI_molecules == "none"
& dat3$Found_in_parents_BSSSI_molecules == "-")
| (dat3$Found_in_parents_BSPQI_molecules == "-"
& dat3$Found_in_parents_BSSSI_molecules == "none"))), ]
dat11 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-")
| (dat3$Found_in_self_BSPQI_molecules == "-"
& dat3$Found_in_self_BSSSI_molecules == "yes"))
& ((dat3$Found_in_parents_BSPQI_molecules == "both"
& dat3$Found_in_parents_BSSSI_molecules == "both")
| (dat3$Found_in_parents_BSPQI_molecules == "-"
& dat3$Found_in_parents_BSSSI_molecules == "both")
| (dat3$Found_in_parents_BSPQI_molecules == "both"
& dat3$Found_in_parents_BSSSI_molecules == "-")
| (dat3$Found_in_parents_BSPQI_molecules == "both"
& dat3$Found_in_parents_BSSSI_molecules == "mother")
| (dat3$Found_in_parents_BSPQI_molecules == "mother"
& dat3$Found_in_parents_BSSSI_molecules == "both")
| (dat3$Found_in_parents_BSPQI_molecules == "both"
& dat3$Found_in_parents_BSSSI_molecules == "father")
| (dat3$Found_in_parents_BSPQI_molecules == "father"
& dat3$Found_in_parents_BSSSI_molecules == "both"))),]
dat12 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-")
| (dat3$Found_in_self_BSPQI_molecules == "-"
& dat3$Found_in_self_BSSSI_molecules == "yes"))
& ((dat3$Found_in_parents_BSPQI_molecules == "mother"
& dat3$Found_in_parents_BSSSI_molecules == "mother")
| (dat3$Found_in_parents_BSPQI_molecules == "-"
& dat3$Found_in_parents_BSSSI_molecules == "mother")
| (dat3$Found_in_parents_BSPQI_molecules == "mother"
& dat3$Found_in_parents_BSSSI_molecules == "-"))), ]
dat13 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-")
| (dat3$Found_in_self_BSPQI_molecules == "-"
& dat3$Found_in_self_BSSSI_molecules == "yes"))
& ((dat3$Found_in_parents_BSPQI_molecules == "father"
& dat3$Found_in_parents_BSSSI_molecules == "father")
| (dat3$Found_in_parents_BSPQI_molecules == "-"
& dat3$Found_in_parents_BSSSI_molecules == "father")
| (dat3$Found_in_parents_BSPQI_molecules == "father"
& dat3$Found_in_parents_BSSSI_molecules == "-"))), ]
dat14 <- rbind(dat12, dat13)
gg <- grep("inversion", as.character(data$Type))
dat8 <- data[gg, ]
dat8 <- dat8[which(((dat8$Found_in_self_BSPQI_molecules == "yes"
& dat8$Found_in_self_BSSSI_molecules == "yes")
| (dat8$Found_in_self_BSPQI_molecules == "no"
& dat8$Found_in_self_BSSSI_molecules == "yes")
| (dat8$Found_in_self_BSPQI_molecules == "yes"
& dat8$Found_in_self_BSSSI_molecules == "no")
| (dat8$Found_in_self_BSPQI_molecules == "yes"
& dat8$Found_in_self_BSSSI_molecules == "-")
| (dat8$Found_in_self_BSPQI_molecules == "-"
& dat8$Found_in_self_BSSSI_molecules == "yes"))
& ((dat8$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat8$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "fail"
& dat8$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat8$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat8$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "-"
& dat8$Fail_BSSSI_assembly_chimeric_score == "pass")
)), ]
gg1 <- grep("translocation", as.character(data$Type))
dat7 <- data[gg1, ]
dat7 <- dat7[which(((dat7$Found_in_self_BSPQI_molecules == "yes"
& dat7$Found_in_self_BSSSI_molecules == "yes")
| (dat7$Found_in_self_BSPQI_molecules == "no"
& dat7$Found_in_self_BSSSI_molecules == "yes")
| (dat7$Found_in_self_BSPQI_molecules == "yes"
& dat7$Found_in_self_BSSSI_molecules == "no")
| (dat7$Found_in_self_BSPQI_molecules == "yes"
& dat7$Found_in_self_BSSSI_molecules == "-")
| (dat7$Found_in_self_BSPQI_molecules == "-"
& dat7$Found_in_self_BSSSI_molecules == "yes"))
& ((dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "fail"
& dat7$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "-"
& dat7$Fail_BSSSI_assembly_chimeric_score == "pass"))), ]
dat6 <- data[which(data$Type %in% "MisMatch"), ]
dat14 <- rbind(dat12, dat13)
ovrlapPG <- which(!((as.character(data$Overlap_PG)=="-")))
datovrlapPG <- data[ovrlapPG,]
nonovrlapupPG <- which(!((as.character(data$Non_Overlap_UP_PG)=="-")))
datnonovrlapUPPG <- data[nonovrlapupPG,]
nonovrlapdnPG <- which(!((as.character(data$Non_Overlap_DN_PG)=="-")))
datnonovrlapDNPG <- data[nonovrlapdnPG,]
datOvrLap <- rbind(datovrlapPG,datnonovrlapUPPG,datnonovrlapDNPG)
'list_of_datasets <- list(
"all" = data, "indel_dup_denovo" = dat10,
"indel_dup_both" = dat11,
"indel_dup_mother" = dat12, "indel_dup_father" = dat13,
"indel_dup_cmpdHET" = dat14, "inv" = dat8, "trans" = dat7, "mismatch" = dat6,
"all_PG_OV" = datovrlapPG, "all_PG_Non_OV_UP" = datnonovrlapUPPG,"all_PG_Non_OV_DN" = datnonovrlapDNPG
)'
if (outputType == "Excel"){
list_of_datasets <- list(
"indel_dup_denovo" = dat10,
"indel_dup_both" = dat11, "indel_dup_cmpdHET" = dat14,
"inv" = dat8, "trans" = dat7,
"indel_dup_mother" = dat12, "indel_dup_father" = dat13,
"all_PG_OV" = datOvrLap, "mismatch" = dat6, "all" = data
)
fname <- paste(outputFilename, ".xlsx", sep = "")
write.xlsx(list_of_datasets, file = file.path(outpath, fname), keepNA = TRUE)
} else if (outputType == "csv"){
write.csv(dat10, file.path(directoryName, paste(
fileprefix,"_indel_dup.csv",sep = "")), row.names = FALSE)
write.csv(dat11, file.path(directoryName, paste(
fileprefix,"_indel_dup_both.csv",sep = "")), row.names = FALSE)
write.csv(dat14, file.path(directoryName, paste(
fileprefix,"_indel_dup_cmpdHET.csv",sep = "")), row.names = FALSE)
write.csv(dat8, file.path(directoryName, paste(
fileprefix,"_inv.csv",sep = "")), row.names = FALSE)
write.csv(dat7, file.path(directoryName, paste(
fileprefix,"_trans.csv",sep = "")), row.names = FALSE)
write.csv(dat12, file.path(directoryName, paste(
fileprefix,"_indel_dup_mother.csv",sep = "")), row.names = FALSE)
write.csv(dat13, file.path(directoryName, paste(
fileprefix,"_indel_dup_father.csv",sep = "")), row.names = FALSE)
write.csv(datOvrLap, file.path(directoryName, paste(
fileprefix,"_all_PG_OV.csv",sep = "")), row.names = FALSE)
write.csv(dat6, file.path(directoryName, paste(
fileprefix,"_mismatch.csv",sep = "")), row.names = FALSE)
write.csv(data, file.path(directoryName, paste(
fileprefix,"_all.csv",sep = "")), row.names = FALSE)
} else {stop(" outputType incorrect !!")}
# gg<-grep("inversion",as.character(data$Type))
# dat8<-data[gg,]
# gg1<-grep("translocation",as.character(data$Type))
# dat7<-data[gg1,]
# dat6<-data[which(data$Type %in% "MisMatch"),]
# list_of_datasets <- list("all" = data, "indel" = dat3, "indel_denovo"= dat10, "indel_both"= dat11,
#"indel_mother"= dat12, "indel father"= dat13, "indel_cmpdHET"=dat14, "inv"= dat8, "trans"=dat7, "mismatch"=dat6,
# "all_PG_OV"=data, "all_PG_Non_OV"= data)
# st1<-strsplit(smap,".txt")[[1]][1]
}
### Running the code
### Copy this 1 line at a time without the hash (#)
### Warning1: Don't remove the # from before the command from filterread.r
### Warning2: give the fullpath with filename for theR code
# source("Z:\\bionano\\Test_R_Codes\\filterread.r")##path of where the Rcode is
#
# run_bionano_filter(path,smap,fileName)
VilainLab/Nanotator documentation built on Oct. 9, 2021, 8:59 p.m.
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Defines functions run_bionano_filter_SVMerge_Trio
Documented in run_bionano_filter_SVMerge_Trio
#' Getting the data from annotated smaps to extract SV
#' information based on type of variants.
#'
#' @param input_fmt_geneList character. Choice of gene list input
#' Text or Dataframe.
#' @param input_fmt_SV character. Choice of gene list input
#' Text or Dataframe.
#' @param smap character. SV file name.
#' @param svData Dataframe Input data containing SV data.
#' @param dat_geneList Dataframe Input data containing geneList data.
#' @param fileName Character Name of file containing Gene List data.
#' @param outpath Character Directory to the output file.
#' @param outputFilename Character Output filename.
#' @param RZIPpath Character Path for the Rtools Zip package.
#' @param outputType Character. Variants in excel tabs or in different csv files.
#' Options Excel or csv.
#' @param EnzymeType Character. Enzyme type used. Options SVMerge or SE.
#' @param fileprefix Character. fileprefix to use for each of the files in the directory.
#' @param directoryName Character. Directory name where individual SV files will be stored.
#' @param primaryGenesPresent boolean Checks whether the primary gene List is present or not.
#' @return Excel file containing the annotated SV map, tabs divided based on
#' type of SVs.
#' @examples
#' \dontrun{
#' smapName <- "GM24385_DLE-1_P_trio_hg19.smap"
#' outputFilename <- "GM24385_DLE-1_P_trio_hg19_out"
#' smappath <- system.file("extdata", smapName, package = "nanotatoR")
#' outpath <- system.file("extdata", smapName, package = "nanotatoR")
#' RZIPpath <- system.file("extdata", "zip.exe", package = "nanotatoR")
#' run_bionano_filter_SVMerge_Trio (input_fmt_geneList = c("Text"),
#' input_fmt_SV = c("Text"),
#' smap = smappath,
#' dat_geneList = dat_geneList,
#' RZIPpath = RZIPpath, EnzymeType = c("SVMerge"),
#' outputType = c("Excel"),
#' primaryGenesPresent = FALSE,
#' outputFilename = outputFilename,
#' outpath = outpath)#' }
#' @import openxlsx
#' @import hash
#' @importFrom stats na.omit
#' @export
run_bionano_filter_SVMerge_Trio <- function(
input_fmt_geneList = c("Text", "dataFrame"),
input_fmt_SV = c("Text", "dataFrame"),
EnzymeType = c("SVMerge", "SE"),
smap = NULL, svData, dat_geneList, fileName, outpath,
outputFilename = "", RZIPpath, primaryGenesPresent = TRUE,
outputType = c("Excel", "csv"), directoryName, fileprefix) {
# library(openxlsx)
# library(hash)
# setwd(path)##change the directory to your working directory
Sys.setenv("R_ZIPCMD" = RZIPpath)
## GeneList Input Format
ha <- hash()
# ll<-list.files(pattern="txt")
if(input_fmt_SV=="dataFrame"){
smapdata = svData
if(EnzymeType == "SVMerge"){
#smapdata <- readSMap(smap, input_fmt_smap = "Text")
SVID<-smapdata$SVIndex
}
else{
#smapdata <- readSMap_DLE(smap, input_fmt_smap)
SVID<-smapdata$SmapEntryID
}
}
else if(input_fmt_SV=="Text"){
if(EnzymeType == "SVMerge"){
smapdata <- readSMap(smap, input_fmt_smap = "Text")
SVID<-smapdata$SVIndex
}
else{
smapdata <- readSMap_DLE(smap, input_fmt_smap = "Text")
SVID<-smapdata$SmapEntryID
}
}
else{
stop("Input format for SMAP Incorrect")
}
r <- smapdata
primaryGenesPresent = primaryGenesPresent
if (primaryGenesPresent == TRUE){
if (input_fmt_geneList == "Text") {
rr <- read.table(fileName, header = TRUE)
}
else if (input_fmt_geneList == "dataFrame") {
rr <- dat_geneList
}
else {
stop("input_fmt_geneList Incorrect!!")
}
ogene <- as.character(r$OverlapGenes_strand_perc)
upgene <- as.character(r$Upstream_nonOverlapGenes_dist_kb)
dngene <- as.character(r$Downstream_nonOverlapGenes_dist_kb)
# nogene<-c(upgene,dngene)
### OverlapGene
dataPGOV <- overlappingGenes (rr, ogene)
### Non-Overlap Up-stream Gene
dataPGUP <- nonOverlappingUPGenes (rr, upgene)
### Non-Overlap Down-stream Gene
dataPGDN <- nonOverlappingDNGenes (rr, dngene)
### Non-OverlapDnGene
# len<-length(pagene)-length(pg)
# genesPG<-c(as.character(pg),rep("-",len))
data <- data.frame(cbind(
r, Overlap_PG = as.character(dataPGOV$pagene),
Overlap_Terms = as.character(dataPGOV$pagene_term),
Overlap_ClinicalSig = as.character(dataPGOV$pagene_clinSig),
Non_Overlap_UP_PG = as.character(dataPGUP$nopageneup),
Non_Overlap_UP_Terms = as.character(dataPGUP$nopageneup_term),
Non_Overlap_UP_ClinicalSig = as.character(
dataPGUP$nopageneup_clinSig),
Non_Overlap_DN_PG = as.character(dataPGDN$nopagenedn),
Non_Overlap_DN_Terms = as.character(dataPGDN$nopagenedn_term),
Non_Overlap_DN_ClinicalSig = as.character(
dataPGDN$nopagenedn_clinSig)))
}else if (primaryGenesPresent == FALSE){
data <- smapdata
}else {stop("primaryGenesPresent Incorrect!!")}
##
data$BNG_Freq_Perc_Filtered<-gsub("-", 0, as.character(
data$BNG_Freq_Perc_Filtered))
data$BNG_Freq_Perc_UnFiltered<-gsub("-",0,as.character(
data$BNG_Freq_Perc_UnFiltered))
data$DGV_Freq_Perc<-as.numeric(data$DGV_Freq_Perc)
data$Internal_Freq_Perc_Filtered<-as.numeric(
data$Internal_Freq_Perc_Filtered)
data$Internal_Freq_Perc_Unfiltered<-as.numeric(
data$Internal_Freq_Perc_Unfiltered)
data$BNG_Freq_Perc_Filtered<-as.numeric(data$BNG_Freq_Perc_Filtered)
data$BNG_Freq_Perc_UnFiltered<-as.numeric(data$BNG_Freq_Perc_UnFiltered)
data$DECIPHER_Frequency<-as.numeric(data$DECIPHER_Frequency)
data$Type1<-as.character(data$Type1)
data$Type2<-as.character(data$Type2)
dat <- data[which(data$Type %in% "insertion"), ]
dat1 <- data[which(data$Type %in% "deletion"), ]
dat44 <- data[which(data$Type %in% "duplication"), ]
dat45 <- data[which(data$Type %in% "duplication_split"), ]
dat46 <- data[which(data$Type %in% "duplication_inverted"), ]
dat_dup_rem<-rbind(dat44,dat45,dat46)
dat_dup_rem_FINAL<-dat_dup_rem[which(((
dat_dup_rem$Type %in% "duplication")
| (dat_dup_rem$Type %in% "duplication_split")
| (dat_dup_rem$Type %in% "duplication_inverted"))
& (((dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "fail"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "-"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass")))), ]
dat3 <- rbind(dat1, dat, dat_dup_rem_FINAL)
dat10 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-")
| (dat3$Found_in_self_BSPQI_molecules == "-"
& dat3$Found_in_self_BSSSI_molecules == "yes"))
& ((dat3$Found_in_parents_BSPQI_molecules == "none"
& dat3$Found_in_parents_BSSSI_molecules == "none")
| (dat3$Found_in_parents_BSPQI_molecules == "none"
& dat3$Found_in_parents_BSSSI_molecules == "-")
| (dat3$Found_in_parents_BSPQI_molecules == "-"
& dat3$Found_in_parents_BSSSI_molecules == "none"))), ]
dat11 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-")
| (dat3$Found_in_self_BSPQI_molecules == "-"
& dat3$Found_in_self_BSSSI_molecules == "yes"))
& ((dat3$Found_in_parents_BSPQI_molecules == "both"
& dat3$Found_in_parents_BSSSI_molecules == "both")
| (dat3$Found_in_parents_BSPQI_molecules == "-"
& dat3$Found_in_parents_BSSSI_molecules == "both")
| (dat3$Found_in_parents_BSPQI_molecules == "both"
& dat3$Found_in_parents_BSSSI_molecules == "-")
| (dat3$Found_in_parents_BSPQI_molecules == "both"
& dat3$Found_in_parents_BSSSI_molecules == "mother")
| (dat3$Found_in_parents_BSPQI_molecules == "mother"
& dat3$Found_in_parents_BSSSI_molecules == "both")
| (dat3$Found_in_parents_BSPQI_molecules == "both"
& dat3$Found_in_parents_BSSSI_molecules == "father")
| (dat3$Found_in_parents_BSPQI_molecules == "father"
& dat3$Found_in_parents_BSSSI_molecules == "both"))),]
dat12 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-")
| (dat3$Found_in_self_BSPQI_molecules == "-"
& dat3$Found_in_self_BSSSI_molecules == "yes"))
& ((dat3$Found_in_parents_BSPQI_molecules == "mother"
& dat3$Found_in_parents_BSSSI_molecules == "mother")
| (dat3$Found_in_parents_BSPQI_molecules == "-"
& dat3$Found_in_parents_BSSSI_molecules == "mother")
| (dat3$Found_in_parents_BSPQI_molecules == "mother"
& dat3$Found_in_parents_BSSSI_molecules == "-"))), ]
dat13 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no")
| (dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-")
| (dat3$Found_in_self_BSPQI_molecules == "-"
& dat3$Found_in_self_BSSSI_molecules == "yes"))
& ((dat3$Found_in_parents_BSPQI_molecules == "father"
& dat3$Found_in_parents_BSSSI_molecules == "father")
| (dat3$Found_in_parents_BSPQI_molecules == "-"
& dat3$Found_in_parents_BSSSI_molecules == "father")
| (dat3$Found_in_parents_BSPQI_molecules == "father"
& dat3$Found_in_parents_BSSSI_molecules == "-"))), ]
dat14 <- rbind(dat12, dat13)
gg <- grep("inversion", as.character(data$Type))
dat8 <- data[gg, ]
dat8 <- dat8[which(((dat8$Found_in_self_BSPQI_molecules == "yes"
& dat8$Found_in_self_BSSSI_molecules == "yes")
| (dat8$Found_in_self_BSPQI_molecules == "no"
& dat8$Found_in_self_BSSSI_molecules == "yes")
| (dat8$Found_in_self_BSPQI_molecules == "yes"
& dat8$Found_in_self_BSSSI_molecules == "no")
| (dat8$Found_in_self_BSPQI_molecules == "yes"
& dat8$Found_in_self_BSSSI_molecules == "-")
| (dat8$Found_in_self_BSPQI_molecules == "-"
& dat8$Found_in_self_BSSSI_molecules == "yes"))
& ((dat8$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat8$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "fail"
& dat8$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat8$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat8$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "-"
& dat8$Fail_BSSSI_assembly_chimeric_score == "pass")
)), ]
gg1 <- grep("translocation", as.character(data$Type))
dat7 <- data[gg1, ]
dat7 <- dat7[which(((dat7$Found_in_self_BSPQI_molecules == "yes"
& dat7$Found_in_self_BSSSI_molecules == "yes")
| (dat7$Found_in_self_BSPQI_molecules == "no"
& dat7$Found_in_self_BSSSI_molecules == "yes")
| (dat7$Found_in_self_BSPQI_molecules == "yes"
& dat7$Found_in_self_BSSSI_molecules == "no")
| (dat7$Found_in_self_BSPQI_molecules == "yes"
& dat7$Found_in_self_BSSSI_molecules == "-")
| (dat7$Found_in_self_BSPQI_molecules == "-"
& dat7$Found_in_self_BSSSI_molecules == "yes"))
& ((dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "fail"
& dat7$Fail_BSSSI_assembly_chimeric_score == "pass")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "-"
& dat7$Fail_BSSSI_assembly_chimeric_score == "pass"))), ]
dat6 <- data[which(data$Type %in% "MisMatch"), ]
dat14 <- rbind(dat12, dat13)
ovrlapPG <- which(!((as.character(data$Overlap_PG)=="-")))
datovrlapPG <- data[ovrlapPG,]
nonovrlapupPG <- which(!((as.character(data$Non_Overlap_UP_PG)=="-")))
datnonovrlapUPPG <- data[nonovrlapupPG,]
nonovrlapdnPG <- which(!((as.character(data$Non_Overlap_DN_PG)=="-")))
datnonovrlapDNPG <- data[nonovrlapdnPG,]
datOvrLap <- rbind(datovrlapPG,datnonovrlapUPPG,datnonovrlapDNPG)
'list_of_datasets <- list(
"all" = data, "indel_dup_denovo" = dat10,
"indel_dup_both" = dat11,
"indel_dup_mother" = dat12, "indel_dup_father" = dat13,
"indel_dup_cmpdHET" = dat14, "inv" = dat8, "trans" = dat7, "mismatch" = dat6,
"all_PG_OV" = datovrlapPG, "all_PG_Non_OV_UP" = datnonovrlapUPPG,"all_PG_Non_OV_DN" = datnonovrlapDNPG
)'
if (outputType == "Excel"){
list_of_datasets <- list(
"indel_dup_denovo" = dat10,
"indel_dup_both" = dat11, "indel_dup_cmpdHET" = dat14,
"inv" = dat8, "trans" = dat7,
"indel_dup_mother" = dat12, "indel_dup_father" = dat13,
"all_PG_OV" = datOvrLap, "mismatch" = dat6, "all" = data
)
fname <- paste(outputFilename, ".xlsx", sep = "")
write.xlsx(list_of_datasets, file = file.path(outpath, fname), keepNA = TRUE)
} else if (outputType == "csv"){
write.csv(dat10, file.path(directoryName, paste(
fileprefix,"_indel_dup.csv",sep = "")), row.names = FALSE)
write.csv(dat11, file.path(directoryName, paste(
fileprefix,"_indel_dup_both.csv",sep = "")), row.names = FALSE)
write.csv(dat14, file.path(directoryName, paste(
fileprefix,"_indel_dup_cmpdHET.csv",sep = "")), row.names = FALSE)
write.csv(dat8, file.path(directoryName, paste(
fileprefix,"_inv.csv",sep = "")), row.names = FALSE)
write.csv(dat7, file.path(directoryName, paste(
fileprefix,"_trans.csv",sep = "")), row.names = FALSE)
write.csv(dat12, file.path(directoryName, paste(
fileprefix,"_indel_dup_mother.csv",sep = "")), row.names = FALSE)
write.csv(dat13, file.path(directoryName, paste(
fileprefix,"_indel_dup_father.csv",sep = "")), row.names = FALSE)
write.csv(datOvrLap, file.path(directoryName, paste(
fileprefix,"_all_PG_OV.csv",sep = "")), row.names = FALSE)
write.csv(dat6, file.path(directoryName, paste(
fileprefix,"_mismatch.csv",sep = "")), row.names = FALSE)
write.csv(data, file.path(directoryName, paste(
fileprefix,"_all.csv",sep = "")), row.names = FALSE)
} else {stop(" outputType incorrect !!")}
# gg<-grep("inversion",as.character(data$Type))
# dat8<-data[gg,]
# gg1<-grep("translocation",as.character(data$Type))
# dat7<-data[gg1,]
# dat6<-data[which(data$Type %in% "MisMatch"),]
# list_of_datasets <- list("all" = data, "indel" = dat3, "indel_denovo"= dat10, "indel_both"= dat11,
#"indel_mother"= dat12, "indel father"= dat13, "indel_cmpdHET"=dat14, "inv"= dat8, "trans"=dat7, "mismatch"=dat6,
# "all_PG_OV"=data, "all_PG_Non_OV"= data)
# st1<-strsplit(smap,".txt")[[1]][1]
}
### Running the code
### Copy this 1 line at a time without the hash (#)
### Warning1: Don't remove the # from before the command from filterread.r
### Warning2: give the fullpath with filename for theR code
# source("Z:\\bionano\\Test_R_Codes\\filterread.r")##path of where the Rcode is
#
# run_bionano_filter(path,smap,fileName)
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