R/interestIntExAnalyzeStranded.R
In gacatag/IntEREst: Intron-Exon Retention Estimator
Defines functions
interestIntExAnalyseSingleStranded
interestIntExAnalysePairStranded
interestIntExAnalysePairStranded <- function(
readTmp,
reference,
maxNoMappedReads,
logFile,
method,
appendLogFile,
repeatsTableToFilter,
referenceIntronExon,
junctionReadsOnly,
limitRanges,
strandSpecific,
excludeFusionReads){
revStr<- c("-", "+", "*")
names(revStr)<- c("+", "-", "*")
qNam<- as.data.frame(GenomicAlignments::first(readTmp))[1,"qname"]
if(logFile!="")
cat( "start ",
qNam, "\n",
file=logFile, append=appendLogFile)
cat( "start ",
qNam, "\n")
if(length(limitRanges)>0){
readTmpFirst<- GenomicAlignments::first(readTmp)
readTmpSecond<- GenomicAlignments::second(readTmp)
if(strandSpecific=="stranded"){
GenomicRanges::strand(readTmpFirst)<-
as.character(GenomicRanges::strand(readTmpFirst))
GenomicRanges::strand(readTmpSecond)<-
revStr[as.character(GenomicRanges::strand(readTmpSecond))]
} else if (strandSpecific=="reverse"){
GenomicRanges::strand(readTmpSecond)<-
as.character(GenomicRanges::strand(readTmpSecond))
GenomicRanges::strand(readTmpFirst)<-
revStr[as.character(GenomicRanges::strand(readTmpFirst))]
}
r1Map<- GenomicRanges::findOverlaps(
readTmpFirst,
limitRanges,
type= "within",
ignore.strand= FALSE)
r2Map<- GenomicRanges::findOverlaps(
readTmpSecond,
limitRanges,
type= "within",
ignore.strand= FALSE)
filLimInd<- sort(unique(intersect(S4Vectors::queryHits(r1Map),
S4Vectors::queryHits(r2Map))),
decreasing=FALSE)
filExtra<- c()
if(excludeFusionReads){
r1LimReads<- tapply(queryHits(r1Map),subjectHits(r1Map), unique)
r2LimReads<- tapply(queryHits(r2Map),subjectHits(r2Map), unique)
commonSubjects<- intersect(names(r1LimReads), names(r2LimReads))
filExtraTmp<- lapply(commonSubjects,
function(x) return (
intersect(r1LimReads[[x]], r2LimReads[[x]])
))
filExtra<- unique(unlist(filExtraTmp))
if(length(filExtra[which(!is.na(filExtra))])>0)
filLimInd<- intersect(filLimInd, filExtra)
}
readTmp<- readTmp[filLimInd,]
}
filStrandInd<-which ( xor(
(as.data.frame(GenomicAlignments::first(readTmp))[,"strand"]=="+") ,
(as.data.frame(GenomicAlignments::second(readTmp))[,"strand"]=="+") ))
readTmp<- readTmp[filStrandInd,]
sam1<- as.data.frame(GenomicAlignments::first(readTmp))[,
c("qname", "rname", "strand", "pos", "qual", "cigar")]
sam2<- as.data.frame(GenomicAlignments::second(readTmp))[,
c("qname", "rname", "strand", "pos", "qual", "cigar")]
colnames(sam1)<- c("qName","rName","strand","pos","qual",
"cigar")
colnames(sam2)<- c("qName","rName","strand","pos","qual",
"cigar")
# if(logFile!="")
# cat( "Analyzing paired reads, ID: ", sam1[1,"qName"], "\n",
# file=logFile, append=appendLogFile)
# cat( "Analyzing paired reads, ID: ", sam1[1,"qName"], "\n")
######
######!!!
exExRes<- c()
intRetRes<- c()
intSpanRes<- c()
exSkipRes<- c()
if(length(readTmp)>0) {
if( length(which(method %in% c("IntRet","ExEx")))>0 ){
######!!!
######
lenRead1= unlist(lapply(sam1$cigar, function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
lenRead2= unlist(lapply(sam2$cigar, function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1=sam1[,"pos"]
chrRead1=sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2=sam2[,"rName"]
locRead2=sam2[,"pos"]
strRead2=sam2[,"strand"]
if(strandSpecific=="stranded"){
strAdj1<- as.character(strRead1)
strAdj2<- as.character(revStr[strRead2])
} else if (strandSpecific=="reverse"){
strAdj2<- as.character(strRead2)
strAdj1<- as.character(revStr[strRead1])
}
frqEventRead1<- lapply(1:length(sam1$cigar), function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
,split="")))]
frqEventTmp=frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
return( list(readNo=rep(tmp,length(frqEventTmpM)),
chr=rep(chrRead1[tmp],length(frqEventTmpM)),
frqEventTmpM, begEventTmpM, endEventTmpM,
str=rep(strRead1[tmp],length(frqEventTmpM))) )
})
frqEventRead2<- lapply(1:length(sam2$cigar), function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam2$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam2$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam2$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead2[tmp], locRead2[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
return(list(readNo=rep(tmp,length(frqEventTmpM)),
chr=rep(chrRead2[tmp],length(frqEventTmpM)),
frqEventTmpM, begEventTmpM, endEventTmpM,
str=rep(strRead2[tmp],length(frqEventTmpM))))
})
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[2]])))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[6]])))))
noRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[1]]))))
chrRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
as.character(unlist(tmp[[2]])))))
begRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[4]]))))
endRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[5]]))))
strRead2=as.vector(unlist(sapply(frqEventRead2, function(tmp)
as.character(unlist(tmp[[6]])))))
if(strandSpecific=="stranded"){
strAdj1<- as.character(strRead1)
strAdj2<- as.character(revStr[strRead2])
} else if (strandSpecific=="reverse"){
strAdj2<- as.character(strRead2)
strAdj1<- as.character(revStr[strRead1])
}
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec=c(as.character(strAdj1),
as.character(strAdj2))
methodNo=which(method=="ExEx")
if(length(methodNo)>0){
ref=reference[which(referenceIntronExon=="exon"),]
#if(strandSpecific%in%c("stranded","reverse")){
# FOR READ1
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1), strand=ref[,"strand"])
if(logFile!="")
cat( "Part1 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits1_1 <- GenomicRanges::findOverlaps(read1GRanges, refGRanges,
type= "start", ignore.strand=FALSE)
if(logFile!="")
cat( "Part2 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits1_2 <- GenomicRanges::findOverlaps(read1GRanges, refGRanges,
type= "end", ignore.strand=FALSE)
if(logFile!="")
cat( "Part3 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits1_3 <- GenomicRanges::findOverlaps(read1GRanges, refGRanges,
type= "equal", ignore.strand=FALSE)
if(logFile!="")
cat( "Part4 ",qNam, "\n",
file=logFile, append=appendLogFile)
# FOR READ2
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2,
end=endRead2),
strand=strAdj2)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"],
end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1),
strand=ref[,"strand"])
if(logFile!="")
cat( "Part1 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits2_1 <- GenomicRanges::findOverlaps(read2GRanges, refGRanges,
type= "start", ignore.strand=FALSE)
if(logFile!="")
cat( "Part2 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits2_2 <- GenomicRanges::findOverlaps(read2GRanges, refGRanges,
type= "end",
ignore.strand=FALSE)
if(logFile!="")
cat( "Part3 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits2_3 <- GenomicRanges::findOverlaps(read2GRanges, refGRanges,
type= "equal",
ignore.strand=FALSE)
if(logFile!="")
cat( "Part4 ",qNam, "\n",
file=logFile, append=appendLogFile)
hitsSubject<- c()
hitsQuery<- c()
hits1Subject=c()
hits1Query=c()
hits2Subject=c()
hits2Query=c()
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter= GenomicRanges::findOverlaps(read1GRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
filtInd1_1= which(is.na(match(S4Vectors::queryHits(hits1_1),
S4Vectors::queryHits(hitsFilter))))
filtInd1_2= which(is.na(match(S4Vectors::queryHits(hits1_2),
S4Vectors::queryHits(hitsFilter))))
filtInd1_3= which(is.na(match(S4Vectors::queryHits(hits1_3),
S4Vectors::queryHits(hitsFilter))))
hitsFilter= GenomicRanges::findOverlaps(read2GRanges,
repeatGRanges, type= "any",
ignore.strand=TRUE)
filtInd2_1= which(is.na(match(S4Vectors::queryHits(hits2_1),
S4Vectors::queryHits(hitsFilter))))
filtInd2_2= which(is.na(match(S4Vectors::queryHits(hits2_2),
S4Vectors::queryHits(hitsFilter))))
filtInd2_3= which(is.na(match(S4Vectors::queryHits(hits2_3),
S4Vectors::queryHits(hitsFilter))))
hits1_1= hits1_1[filtInd1_1,]
hits1_2= hits1_2[filtInd1_2,]
hits1_3= hits1_3[filtInd1_3,]
hits2_1= hits2_1[filtInd2_1,]
hits2_2= hits2_2[filtInd2_2,]
hits2_3= hits2_3[filtInd2_3,]
}
# Include the reads that completely map to exons if user asked
if(!junctionReadsOnly){
hits1Extra= GenomicRanges::findOverlaps(read1GRanges,
refGRanges, type= "within", ignore.strand=FALSE)
hits2Extra= GenomicRanges::findOverlaps(read2GRanges,
refGRanges, type= "within", ignore.strand=FALSE)
hits1Subject=S4Vectors::subjectHits(hits1Extra)
hits1Query=S4Vectors::queryHits(hits1Extra)
hits2Subject=S4Vectors::subjectHits(hits2Extra)
hits2Query=S4Vectors::queryHits(hits2Extra)
}
hits1Subject=c(hits1Subject, S4Vectors::subjectHits(hits1_1),
S4Vectors::subjectHits(hits1_2),S4Vectors::subjectHits(hits1_3))
hits2Subject=c(hits2Subject, S4Vectors::subjectHits(hits2_1),
S4Vectors::subjectHits(hits2_2),S4Vectors::subjectHits(hits2_3))
if(logFile!="")
cat( "Part5 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits1Query=c(hits1Query, S4Vectors::queryHits(hits1_1),
S4Vectors::queryHits(hits1_2), S4Vectors::queryHits(hits1_3))
hits2Query=c(hits2Query, S4Vectors::queryHits(hits2_1),
S4Vectors::queryHits(hits2_2), S4Vectors::queryHits(hits2_3))
if(logFile!="")
cat( "Part6 ",qNam, "\n",
file=logFile, append=appendLogFile)
refRes= rep(0,nrow(ref))
if(length(hits1Query)>0){
hitsApply= tapply(c(noRead1[hits1Query], noRead2[hits2Query]),
c(hits1Subject, hits2Subject),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
if(logFile!="")
cat( "Part7 ",qNam, "\n",
file=logFile, append=appendLogFile)
exExRes<-rep(0, nrow(reference))
exExRes[which(referenceIntronExon=="exon")]<- refRes
rm("refRes")
}
methodNo=which(method=="IntRet")
if((length(methodNo)>0) & (! junctionReadsOnly)){
ref=reference[which(referenceIntronExon=="intron"),]
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2, end=endRead2), strand=strAdj2)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"],
end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1),
strand=ref[,"strand"])
hits1 <- GenomicRanges::findOverlaps(read1GRanges, refGRanges,
type= "any", ignore.strand=FALSE)
hits2 <- GenomicRanges::findOverlaps(read2GRanges, refGRanges,
type= "any", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter1= GenomicRanges::findOverlaps(read1GRanges,
repeatGRanges, type= "any",ignore.strand=TRUE)
hitsFilter2= GenomicRanges::findOverlaps(read2GRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
# Explanation: If both reads have regions overlapping repeat regions ignore them!
filNoHits<-
unique(intersect(noRead1[queryHits(hitsFilter1)],
noRead2[queryHits(hitsFilter2)]))
filtInd1=
which( !(noRead1[S4Vectors::queryHits(hits1)] %in% filNoHits))
filtInd2=
which( !(noRead2[S4Vectors::queryHits(hits2)] %in% filNoHits))
hits1=hits1[filtInd1,]
hits2=hits2[filtInd2,]
}
refRes= rep(0,nrow(ref))
if(length(S4Vectors::queryHits(hits1))>0 | length(S4Vectors::queryHits(hits2))>0){
hitsApply=tapply(
c(noRead1[S4Vectors::queryHits(hits1)],
noRead2[S4Vectors::queryHits(hits2)]),
c(S4Vectors::subjectHits(hits1), S4Vectors::subjectHits(hits2)),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(unique(names(hitsApply)))]=
as.vector(hitsApply)
}
intRetRes<- rep(0,nrow(reference))
intRetRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
} else if ((length(methodNo)>0) & (junctionReadsOnly)) {
ref=reference[which(referenceIntronExon=="intron"),]
refEndGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"end"], end=ref[,"end"]),
strand=ref[,"strand"])
refBegGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"begin"]),
strand=ref[,"strand"])
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
hitsEnd1 <- GenomicRanges::findOverlaps(refEndGRanges, read1GRanges,
type= "within", ignore.strand=FALSE)
hitsBeg1 <- GenomicRanges::findOverlaps(refBegGRanges, read1GRanges,
type= "within", ignore.strand=FALSE)
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2, end=endRead2), strand=strAdj2)
hitsEnd2 <- GenomicRanges::findOverlaps(refEndGRanges, read2GRanges,
type= "within", ignore.strand=FALSE)
hitsBeg2 <- GenomicRanges::findOverlaps(refBegGRanges, read2GRanges,
type= "within", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter1= GenomicRanges::findOverlaps(read1GRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
hitsFilter2= GenomicRanges::findOverlaps(read2GRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
noFilQuHits<-
intersect(noRead1[queryHits(hitsFilter1)],
noRead2[queryHits(hitsFilter2)])
filtEndInd1= which(! noRead1[S4Vectors::subjectHits(hitsEnd1)] %in%
noFilQuHits)
filtBegInd1= which(! noRead1[S4Vectors::subjectHits(hitsBeg1)] %in%
noFilQuHits)
filtEndInd2= which(! noRead2[S4Vectors::subjectHits(hitsEnd2)] %in%
noFilQuHits)
filtBegInd2= which(! noRead2[S4Vectors::subjectHits(hitsBeg2)] %in%
noFilQuHits)
hitsEnd1=hitsEnd1[filtEndInd1,]
hitsBeg1=hitsBeg1[filtBegInd1,]
hitsEnd2=hitsEnd2[filtEndInd2,]
hitsBeg2=hitsBeg2[filtBegInd2,]
}
refRes= rep(0,nrow(ref))
refResBeg= refRes
refResEnd= refRes
if( (length(S4Vectors::subjectHits(hitsBeg1))>0) |
(length(S4Vectors::subjectHits(hitsEnd1))>0) |
(length(S4Vectors::subjectHits(hitsBeg2))>0) |
(length(S4Vectors::subjectHits(hitsEnd2))>0) ){
hitsEndApply=tapply(
c(noRead1[S4Vectors::subjectHits(hitsEnd1)],
noRead2[S4Vectors::subjectHits(hitsEnd2)]),
c(S4Vectors::queryHits(hitsEnd1), S4Vectors::queryHits(hitsEnd2)),
function(tmp) return(length(unique(tmp))) )
hitsBegApply=tapply(
c(noRead1[S4Vectors::subjectHits(hitsBeg1)],
noRead2[S4Vectors::subjectHits(hitsBeg2)]),
c(S4Vectors::queryHits(hitsBeg1), S4Vectors::queryHits(hitsBeg2)),
function(tmp) return(length(unique(tmp))) )
refResBeg[as.numeric(names(hitsBegApply))]=
as.numeric(hitsBegApply)
refResEnd[as.numeric(names(hitsEndApply))]=
as.numeric(hitsEndApply)
refRes=refResBeg+refResEnd
rm("refResBeg","refResEnd")
}
intRetRes<- rep(0,nrow(reference))
intRetRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
}
########
########!!!
}
methodNo=which(method=="IntSpan")
if(length(methodNo)>0){
sam1IndSp<- grep("N",sam1$cigar)
sam2IndSp<- grep("N",sam2$cigar)
lenRead1= unlist(lapply(sam1$cigar[sam1IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
lenRead2= unlist(lapply(sam2$cigar[sam2IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1=sam1[,"pos"]
chrRead1=sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2=sam2[,"rName"]
locRead2=sam2[,"pos"]
strRead2=sam2[,"strand"]
frqEventRead1 =lapply(sam1IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead1[tmp],length(frqEventTmpN)) ))
})
frqEventRead2= lapply(sam2IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam2$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam2$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam2$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead2[tmp], locRead2[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead2[tmp],length(frqEventTmpN) )))
})
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[10]])))))
noRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[1]]))))
chrRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[2]]))))
begRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[4]]))))
endRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[5]]))))
strRead2=as.vector(unlist(sapply(frqEventRead2, function(tmp)
as.character(unlist(tmp[[10]])))))
if(strandSpecific=="stranded"){
strAdj1<- as.character(strRead1)
strAdj2<- as.character(revStr[strRead2])
} else if (strandSpecific=="reverse"){
strAdj2<- as.character(strRead2)
strAdj1<- as.character(revStr[strRead1])
}
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec<- c(strAdj1,strAdj2)
ref=reference[which(referenceIntronExon=="intron"),]
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2, end=endRead2), strand=strAdj2)
# refIntBegGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
# IRanges::IRanges(start=ref[,"begin"]-1, end=ref[,"begin"]-1),
# strand=ref[,"strand"])
# refIntEndGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
# IRanges::IRanges(start=ref[,"end"]+1, end=ref[,"end"]+1),
# strand=ref[,"strand"])
refIntGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"]),
strand=ref[,"strand"])
### !!!
### THIS IS NOT THE BEST WAY. WHY SEPARATE ON BEGIN AND END ?
###WHY NOT hitsBegInt <- GenomicRanges::findOverlaps(readGRanges,
### refIntGRanges, type= "equal")
# hitsBegInt1 <- GenomicRanges::findOverlaps(read1GRanges,
# refIntBegGRanges, type= "end", ignore.strand=FALSE)
# hitsEndInt1 <- GenomicRanges::findOverlaps(read1GRanges,
# refIntEndGRanges, type= "start", ignore.strand=FALSE)
# hitsBegInt2 <- GenomicRanges::findOverlaps(read2GRanges,
# refIntBegGRanges, type= "end", ignore.strand=FALSE)
# hitsEndInt2 <- GenomicRanges::findOverlaps(read2GRanges,
# refIntEndGRanges, type= "start", ignore.strand=FALSE)
hitsInt1 <- GenomicRanges::findOverlaps(read1GRanges,
refIntGRanges, type= "equal", ignore.strand=FALSE)
hitsInt2 <- GenomicRanges::findOverlaps(read2GRanges,
refIntGRanges, type= "equal", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
# if(length(repeatsTableToFilter)!=0){
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# hitsFilter1= GenomicRanges::findOverlaps(read1GRanges,
# repeatGRanges, type= "any", ignore.strand=TRUE)
# hitsFilter2= GenomicRanges::findOverlaps(read2GRanges,
# repeatGRanges, type= "any", ignore.strand=TRUE)
#
# noFilQuHits<-
# intersect(noRead1[queryHits(hitsFilter1)],
# noRead2[queryHits(hitsFilter2)])
#
# filtEndInd1= which(! noRead1[S4Vectors::subjectHits(hitsEndInt1)] %in%
# noFilQuHits)
# filtBegInd1= which(! noRead1[S4Vectors::subjectHits(hitsBegInt1)] %in%
# noFilQuHits)
#
# filtEndInd2= which(! noRead2[S4Vectors::subjectHits(hitsEndInt2)] %in%
# noFilQuHits)
# filtBegInd2= which(! noRead2[S4Vectors::subjectHits(hitsBegInt2)] %in%
# noFilQuHits)
#
#
# hitsBegInt1=hitsBegInt1[filtBegInd1,]
# hitsEndInt1=hitsEndInt1[filtEndInd1,]
# hitsBegInt2=hitsBegInt2[filtBegInd2,]
# hitsEndInt2=hitsEndInt2[filtEndInd2,]
# }
# if(length(repeatsTableToFilter)!=0){
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# hitsFilter1= GenomicRanges::findOverlaps(read1GRanges,
# repeatGRanges, type= "equal", ignore.strand=TRUE)
# hitsFilter2= GenomicRanges::findOverlaps(read2GRanges,
# repeatGRanges, type= "equal", ignore.strand=TRUE)
#
# noFilQuHits<-
# intersect(noRead1[queryHits(hitsFilter1)],
# noRead2[queryHits(hitsFilter2)])
#
# filtInd1= which(! noRead1[S4Vectors::subjectHits(hitsInt1)] %in%
# noFilQuHits)
#
# filtEndInd2= which(! noRead2[S4Vectors::subjectHits(hitsInt2)] %in%
# noFilQuHits)
#
# hitsInt1=hitsInt1[filtInd1,]
# hitsInt2=hitsInt2[filtInd2,]
# }
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
# if(length(c(S4Vectors::queryHits(hitsBegInt1),
# S4Vectors::queryHits(hitsEndInt1)))>0 |
# length(c(S4Vectors::queryHits(hitsBegInt2),
# S4Vectors::queryHits(hitsEndInt2)))>0){
# hitsApply=tapply(
# c(noRead1[c(S4Vectors::queryHits(hitsBegInt1),
# S4Vectors::queryHits(hitsEndInt1))],
# noRead2[c(S4Vectors::queryHits(hitsBegInt2),
# S4Vectors::queryHits(hitsEndInt2))]),
# c(S4Vectors::subjectHits(hitsBegInt1),
# S4Vectors::subjectHits(hitsEndInt1),
# S4Vectors::subjectHits(hitsBegInt2),
# S4Vectors::subjectHits(hitsEndInt2)),
# function(tmp) return(length(unique(tmp))) )
# refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
# }
if(length(S4Vectors::queryHits(hitsInt1))>0 |
length(S4Vectors::queryHits(hitsInt2))>0){
hitsApply=tapply(
c(noRead1[S4Vectors::queryHits(hitsInt1)],
noRead2[S4Vectors::queryHits(hitsInt2)]),
c(S4Vectors::subjectHits(hitsInt1),
S4Vectors::subjectHits(hitsInt2)),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
intSpanRes<- rep(0,nrow(reference))
intSpanRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
}
####
### NEW ExSkip
methodNo=which(method=="ExSkip")
if(length(methodNo)>0){
sam1IndSp<- grep("N",sam1$cigar)
sam2IndSp<- grep("N",sam2$cigar)
lenRead1= unlist(lapply(sam1$cigar[sam1IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
lenRead2= unlist(lapply(sam2$cigar[sam2IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1=sam1[,"pos"]
chrRead1=sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2=sam2[,"rName"]
locRead2=sam2[,"pos"]
strRead2=sam2[,"strand"]
frqEventRead1 =lapply(sam1IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead1[tmp],length(frqEventTmpN)) ))
})
frqEventRead2= lapply(sam2IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam2$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam2$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam2$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead2[tmp], locRead2[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead2[tmp],length(frqEventTmpN) )))
})
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[10]])))))
noRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[1]]))))
chrRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[2]]))))
begRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[4]]))))
endRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[5]]))))
strRead2=as.vector(unlist(sapply(frqEventRead2, function(tmp)
as.character(unlist(tmp[[10]])))))
if(strandSpecific=="stranded"){
strAdj1<- as.character(strRead1)
strAdj2<- as.character(revStr[strRead2])
} else if (strandSpecific=="reverse"){
strAdj2<- as.character(strRead2)
strAdj1<- as.character(revStr[strRead1])
}
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec<- c(strAdj1,strAdj2)
ref=reference[which(referenceIntronExon=="exon"),]
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2, end=endRead2), strand=strAdj2)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"]),
strand=ref[,"strand"])
hitsAllEx1 <- GenomicRanges::findOverlaps(refGRanges,
read1GRanges, type= "within",
ignore.strand= FALSE)
hitsAllEx2 <- GenomicRanges::findOverlaps(refGRanges,
read2GRanges, type= "within",
ignore.strand= FALSE)
# Filter reads mapped to repeats regions if requested
# if(length(repeatsTableToFilter)!=0){
# noRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[9]]))))
# chrRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[2]]))))
# begRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[7]]))))
# endRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[8]]))))
#
# noRead2M= as.vector(unlist(sapply(frqEventRead2, function(tmp)
# unlist(tmp[[9]]))))
# chrRead2M= as.vector(unlist(sapply(frqEventRead2, function(tmp)
# unlist(tmp[[2]]))))
# begRead2M= as.vector(unlist(sapply(frqEventRead2, function(tmp)
# unlist(tmp[[7]]))))
# endRead2M= as.vector(unlist(sapply(frqEventRead2, function(tmp)
# unlist(tmp[[8]]))))
#
# # analyzing reads
# noVecM=c(noRead1M,noRead2M)
# chrVecM=c(as.character(chrRead1M),
# as.character(chrRead2M))
# begVecM=c(begRead1M,begRead2M)
# endVecM=c(endRead1M,endRead2M)
#
# readGRangesM1=GenomicRanges::GRanges( seqnames=chrRead1M,
# IRanges::IRanges(start=begRead1M, end=endRead1M))
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# hitsFilter1= GenomicRanges::findOverlaps(readGRangesM1,
# repeatGRanges, type= "any", ignore.strand=TRUE)
# hitsFilter2= GenomicRanges::findOverlaps(readGRangesM2,
# repeatGRanges, type= "any", ignore.strand=TRUE)
#
# # noVecFil<- unique(noVecM[queryHits(hitsFilter)])
# # filthitsAllExInd<- which(!subjectHits(hitsAllEx) %in%
# # subjectHits(hitsAllEx)[
# # which(noVec[subjectHits(hitsAllEx)]
# # %in% noVecFil)])
# # hitsAllEx=hitsAllEx[filthitsAllExInd,]
# noFilQuHits<-
# intersect(noRead1[queryHits(hitsFilter1)],
# noRead2[queryHits(hitsFilter2)])
#
# filtAllInd1= which(! noRead1[S4Vectors::subjectHits(hitsAllEx1)] %in%
# noFilQuHits)
# filtAllInd2= which(! noRead1[S4Vectors::subjectHits(hitsAllEx2)] %in%
# noFilQuHits)
#
#
#
# hitsAllEx1=hitsAllEx1[filtAllInd1,]
# hitsAllEx2=hitsAllEx2[filtAllInd2,]
# # hitsBegInt2=hitsBegInt2[filtBegInd2,]
# # hitsEndInt2=hitsEndInt2[filtEndInd2,]
#
# }
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
if(length(c(S4Vectors::subjectHits(hitsAllEx1),
S4Vectors::subjectHits(hitsAllEx2)))>0){
hitsApply=tapply(
c(noRead1[S4Vectors::subjectHits(hitsAllEx1)],
noRead2[S4Vectors::subjectHits(hitsAllEx2)]),
c(S4Vectors::queryHits(hitsAllEx1),
S4Vectors::queryHits(hitsAllEx2)),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
exSkipRes<- rep(0,nrow(reference))
exSkipRes[which(referenceIntronExon=="exon")]<- refRes
rm("refRes")
}
}
########!!!
########
########!!!
########
finalRes<-c()
if(length(exExRes)==0)
exExRes<- rep(0,nrow(reference))
if(length(intRetRes)==0)
intRetRes<- rep(0,nrow(reference))
if(length(intSpanRes)==0)
intSpanRes<- rep(0,nrow(reference))
if(length(exSkipRes)==0)
exSkipRes<- rep(0,nrow(reference))
# if(length(exExRes)>0){
if("ExEx" %in% method)
finalRes<-c(finalRes, exExRes)
rm("exExRes")
# if(length(intRetRes)>0)
if("IntRet" %in% method)
finalRes<-c(finalRes, intRetRes)
rm("intRetRes")
########
########!!!
# if(length(intSpanRes)>0)
if("IntSpan" %in% method)
finalRes<-c(finalRes, intSpanRes)
rm("intSpanRes")
# if(length(exSkipRes)>0)
if("ExSkip" %in% method)
finalRes<-c(finalRes, exSkipRes)
rm("exSkipRes")
########!!!
########
if(logFile!="")
cat( "end ",
qNam, " ", length(finalRes), "\n",
file=logFile, append=appendLogFile)
cat( "end ",
qNam, " ", length(finalRes), "\n")
# if(is.null(finalRes))
# finalRes<- rep(0,
# length(which(method%in%c("ExEx", "IntRet", "IntSpan", "ExSkip"))))
return(finalRes)
rm("finalRes")
#End of defining function for paired-mapped reads that runs on parallel cores
}
# For single reads
interestIntExAnalyseSingleStranded <- function(
readTmp,
reference,
maxNoMappedReads,
logFile,
method,
appendLogFile,
repeatsTableToFilter,
referenceIntronExon,
junctionReadsOnly,
limitRanges,
strandSpecific,
excludeFusionReads)
{
revStr<- c("-", "+", "*")
names(revStr)<- c("+", "-", "*")
qNam<- as.data.frame(readTmp)[1, "qname"]
if(logFile!="")
cat( "Singlestart ",
qNam, "\n",
file=logFile, append=appendLogFile)
cat( "Singlestart ",
qNam, "\n")
# Filtering readTmp based on number of mapping targets for each read
lenTmp<- unlist(sapply(readTmp, length))
readTmpFil<- readTmp[which(lenTmp<= maxNoMappedReads)]
sam2= NA
sam1Flag<- mcols(unlist(readTmpFil))$flag
sam1FlagMat<-bamFlagAsBitMatrix(sam1Flag)
readMate<- rep(1,nrow(sam1FlagMat))
readMate[which(sam1FlagMat[,"isSecondMateRead"]==1)]<- 2
readTmpFirst<- unlist(readTmpFil)
if(strandSpecific=="stranded"){
if(length(which(readMate==1))>0)
GenomicRanges::strand(readTmpFirst)[which(readMate==1)]<-
as.character(GenomicRanges::strand(readTmpFirst)[which(readMate==1)])
if(length(which(readMate==2))>0)
GenomicRanges::strand(readTmpFirst)[which(readMate==2)]<-
as.character(revStr[as.character(GenomicRanges::strand(readTmpFirst))][which(readMate==2)])
} else if (strandSpecific=="reverse"){
if(length(which(readMate==2))>0)
GenomicRanges::strand(readTmpFirst)[which(readMate==2)]<-
as.character(GenomicRanges::strand(readTmpFirst)[which(readMate==2)])
if(length(which(readMate==1))>0)
GenomicRanges::strand(readTmpFirst)[which(readMate==1)]<-
as.character(revStr[as.character(GenomicRanges::strand(readTmpFirst))][which(readMate==1)])
}
if(length(limitRanges)>0 & length(readTmpFirst)>0){
r1Map<- GenomicRanges::findOverlaps(
readTmpFirst,
limitRanges,
type= "within",
ignore.strand= FALSE)
filLimInd<- sort(unique(S4Vectors::queryHits(r1Map)), decreasing=FALSE)
readTmpFirst<- readTmpFirst[filLimInd,]
}
#Extract information of the mapped pieces of the reads
sam1<- as.data.frame(readTmpFirst)[, c("qname", "rname", "strand",
"pos", "qual", "cigar")]
colnames(sam1)<- c("qName","rName","strand","pos","qual",
"cigar")
### Incorporate FLAGS to figure what reads are fisrt or second from mate in singletons
### then adjust strands accordingly.
### Use flags<-bamFlagAsBitMatrix(mcols(unlist(readTmpFil))$flag)
### Column 7 and 8 is first or second mate
### Update what in scanbamwhat with scParam3=Rsamtools::ScanBamParam(
###what=Rsamtools::scanBamWhat()[c(1,
### 3,5,8,13,9, 10, 6, 4, 14, 15, 2)],
# if(logFile!="")
# cat( "Analyzing single reads, ID: ", sam1[1,"qName"], "\n",
# file=logFile, append=appendLogFile)
# cat( "Analyzing single reads, ID: ", sam1[1,"qName"], "\n")
######
######!!!
exExRes<- c()
intRetRes<- c()
intSpanRes<- c()
exSkipRes<- c()
if(length(readTmp)>0){
if( length(which(method %in% c("IntRet","ExEx")))>0 ){
######!!!
######
lenRead1= unlist(lapply(sam1$cigar, function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
lenRead2= 0
locRead1= sam1[,"pos"]
chrRead1= sam1[,"rName"]
chrRead2= 0
locRead2= 0
strRead1=sam1[,"strand"]
strRead2=0
if(strandSpecific=="stranded"){
if(length(which(readMate==2))>0)
strRead1[which(readMate==2)]<-
as.character(revStr[which(readMate==2)])
} else if (strandSpecific=="reverse"){
strRead1[which(readMate==1)]<-
as.character(revStr[strRead1[which(readMate==1)]])
}
frqEventRead1 =lapply(1:length(sam1$cigar), function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
return( list(readNo=rep(tmp,length(frqEventTmpM)),
chr=rep(chrRead1[tmp],length(frqEventTmpM)),
frqEventTmpM, begEventTmpM, endEventTmpM,
strand=rep(strRead1[tmp],length(frqEventTmpM)),
mate=rep(readMate[tmp],length(frqEventTmpM))))
})
frqEventRead2=NA
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[6]])))))
mateRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[7]])))))
noRead2= c()
chrRead2= c()
begRead2= c()
endRead2= c()
strRead2= c()
strRead2= c()
strAdj1<- strRead1
##### HERE 1 !!!!
strAdj2<- c()
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec=c(as.character(strAdj1),
as.character(strAdj2))
exExRes<- c()
intRetRes<- c()
methodNo= which(method=="ExEx")
if(length(methodNo)>0){
ref= reference[which(referenceIntronExon=="exon"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1), strand=ref[,"strand"])
hits1 <- GenomicRanges::findOverlaps(readGRanges, refGRanges,
type= "start", ignore.strand=FALSE)
if(logFile!="")
cat( "Part8 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits2 <- GenomicRanges::findOverlaps(readGRanges, refGRanges,
type= "end", ignore.strand=FALSE)
if(logFile!="")
cat( "Part9 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits3 <- GenomicRanges::findOverlaps(readGRanges, refGRanges,
type= "equal", ignore.strand=FALSE)
if(logFile!="")
cat( "Part10 ",qNam, "\n",
file=logFile, append=appendLogFile)
hitsSubject<- c()
hitsQuery<- c()
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter= GenomicRanges::findOverlaps(readGRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
filtInd1= which(is.na(match(S4Vectors::queryHits(hits1),
S4Vectors::queryHits(hitsFilter))))
filtInd2= which(is.na(match(S4Vectors::queryHits(hits2),
S4Vectors::queryHits(hitsFilter))))
filtInd3= which(is.na(match(S4Vectors::queryHits(hits3),
S4Vectors::queryHits(hitsFilter))))
hits1= hits1[filtInd1,]
hits2= hits2[filtInd2,]
hits3= hits3[filtInd3,]
}
# Include the reads that completely map to exons if user asked
if(!junctionReadsOnly){
hitsExtra= GenomicRanges::findOverlaps(readGRanges,
refGRanges, type= "within", ignore.strand=FALSE)
hitsSubject=S4Vectors::subjectHits(hitsExtra)
hitsQuery=S4Vectors::queryHits(hitsExtra)
}
hitsSubject=c(hitsSubject, S4Vectors::subjectHits(hits1),
S4Vectors::subjectHits(hits2),S4Vectors::subjectHits(hits3))
if(logFile!="")
cat( "Part11 ",qNam, "\n",
file=logFile, append=appendLogFile)
hitsQuery=c(hitsQuery, S4Vectors::queryHits(hits1),
S4Vectors::queryHits(hits2), S4Vectors::queryHits(hits3))
refRes= rep(0,nrow(ref))
if(length(hitsQuery)>0){
hitsApply= tapply(noVec[hitsQuery], hitsSubject, function(tmp)
return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
if(logFile!="")
cat( "Part12 ",qNam, "\n",
file=logFile, append=appendLogFile)
exExRes<-rep(0, nrow(reference))
exExRes[which(referenceIntronExon=="exon")]<- refRes
rm("refRes")
}
methodNo=which(method=="IntRet")
if((length(methodNo)>0) & (! junctionReadsOnly)){
ref=reference[which(referenceIntronExon=="intron"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges(start=ref[,"begin"], end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1), strand=ref[,"strand"])
hits <- GenomicRanges::findOverlaps(readGRanges, refGRanges,
type= "any", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter= GenomicRanges::findOverlaps(readGRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
filtInd= which(is.na(match(S4Vectors::queryHits(hits),
S4Vectors::queryHits(hitsFilter))))
hits=hits[filtInd,]
}
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
if(length(S4Vectors::queryHits(hits))>0){
hitsApply=tapply(noVec[S4Vectors::queryHits(hits)],
S4Vectors::subjectHits(hits),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
intRetRes<- rep(0,nrow(reference))
intRetRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
} else if ((length(methodNo)>0) & (junctionReadsOnly)) {
ref=reference[which(referenceIntronExon=="intron"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
refEndGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"end"], end=ref[,"end"]),
strand=ref[,"strand"])
refBegGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"begin"]),
strand=ref[,"strand"])
hitsEnd <- GenomicRanges::findOverlaps(refEndGRanges, readGRanges,
type= "within", ignore.strand=FALSE)
hitsBeg <- GenomicRanges::findOverlaps(refBegGRanges, readGRanges,
type= "within", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter= GenomicRanges::findOverlaps(readGRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
filtEndInd= which(is.na(match(S4Vectors::subjectHits(hitsEnd),
S4Vectors::queryHits(hitsFilter))))
filtBegInd= which(is.na(match(S4Vectors::subjectHits(hitsBeg),
S4Vectors::queryHits(hitsFilter))))
hitsEnd=hitsEnd[filtEndInd,]
hitsBeg=hitsBeg[filtBegInd,]
}
refRes= rep(0,nrow(ref))
refResBeg= refRes
refResEnd= refRes
if( (length(S4Vectors::subjectHits(hitsBeg))>0) |
(length(S4Vectors::subjectHits(hitsEnd))>0) ){
hitsEndApply=tapply(noVec[S4Vectors::subjectHits(hitsEnd)],
S4Vectors::queryHits(hitsEnd),
function(tmp) return(length(unique(tmp))) )
hitsBegApply=tapply(noVec[S4Vectors::subjectHits(hitsBeg)],
S4Vectors::queryHits(hitsBeg),
function(tmp) return(length(unique(tmp))) )
refResBeg[as.numeric(names(hitsBegApply))]=
as.numeric(hitsBegApply)
refResEnd[as.numeric(names(hitsEndApply))]=
as.numeric(hitsEndApply)
refRes=refResBeg+refResEnd
rm("refResBeg","refResEnd")
}
intRetRes<- rep(0,nrow(reference))
intRetRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
}
}
### HERE !!!
methodNo=which(method=="IntSpan")
if(length(methodNo)>0){
sam1IndSp<- grep("N",sam1$cigar)
sam2IndSp<- c()
lenRead1= unlist(lapply(sam1$cigar[sam1IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1= sam1[,"pos"]
chrRead1= sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2= c()
strRead2=c()
locRead2=c()
if(strandSpecific=="stranded"){
if(length(which(readMate==2))>0)
strRead1[which(readMate==2)]<-
as.character(revStr[which(readMate==2)])
} else if (strandSpecific=="reverse"){
strRead1[which(readMate==1)]<-
as.character(revStr[strRead1[which(readMate==1)]])
}
frqEventRead1 =lapply(sam1IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead1[tmp],length(frqEventTmpN)),
mate=rep(readMate[tmp],length(frqEventTmpN)),
chrM=rep(chrRead1[tmp],length(frqEventTmpM))))
})
frqEventRead2=NA
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[10]])))))
mateRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[11]])))))
noRead2= c()
chrRead2= c()
begRead2= c()
endRead2= c()
strRead2=c()
strAdj1<- strRead1
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec=c(as.character(strAdj1),
as.character(strAdj2))
ref=reference[which(referenceIntronExon=="intron"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
# refIntBegGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
# IRanges::IRanges(start=ref[,"begin"]-1, end=ref[,"begin"]-1),
# strand=ref[,"strand"])
# refIntEndGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
# IRanges::IRanges(start=ref[,"end"]+1, end=ref[,"end"]+1),
# strand=ref[,"strand"])
refIntGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"]),
strand=ref[,"strand"])
### !!!
### THIS IS NOT THE BEST WAY. WHY SEPARATE ON BEGIN AND END ?
###WHY NOT hitsBegInt <- GenomicRanges::findOverlaps(readGRanges,
### refIntGRanges, type= "equal")
# hitsBegInt <- GenomicRanges::findOverlaps(readGRanges,
# refIntBegGRanges, type= "end", ignore.strand=FALSE)
# hitsEndInt <- GenomicRanges::findOverlaps(readGRanges,
# refIntEndGRanges, type= "start", ignore.strand=FALSE)
hitsInt <- GenomicRanges::findOverlaps(readGRanges,
refIntGRanges, type= "equal", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
# if(length(repeatsTableToFilter)!=0){
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# # hitsFilter= GenomicRanges::findOverlaps(readGRanges,
# # repeatGRanges, type= "any", ignore.strand=TRUE)
# # filtBegInd= which(is.na(match(S4Vectors::queryHits(hitsBegInt),
# # S4Vectors::queryHits(hitsFilter))))
# # hitsBegInt=hitsBegInt[filtBegInd,]
# # filtEndInd= which(is.na(match(S4Vectors::queryHits(hitsEndInt),
# # S4Vectors::queryHits(hitsFilter))))
# # hitsEndInt=hitsEndInt[filtEndInd,]
# hitsFilter= GenomicRanges::findOverlaps(readGRanges,
# repeatGRanges, type= "equal", ignore.strand=TRUE)
# filtInd= which(is.na(match(S4Vectors::queryHits(hitsInt),
# S4Vectors::queryHits(hitsFilter))))
# hitsInt=hitsInt[filtInd,]
# }
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
# if(length(c(S4Vectors::queryHits(hitsBegInt),
# S4Vectors::queryHits(hitsEndInt)))>0){
# hitsApply=tapply(
# noVec[c(S4Vectors::queryHits(hitsBegInt),
# S4Vectors::queryHits(hitsEndInt))],
# c(S4Vectors::subjectHits(hitsBegInt),
# S4Vectors::subjectHits(hitsEndInt)),
# function(tmp) return(length(unique(tmp))) )
# refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
# }
if(length(S4Vectors::queryHits(hitsInt))>0){
hitsApply=tapply(
noVec[S4Vectors::queryHits(hitsInt)],
c(S4Vectors::subjectHits(hitsInt)),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
intSpanRes<- rep(0,nrow(reference))
intSpanRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
}
####
### NEW ExSkip
methodNo=which(method=="ExSkip")
if(length(methodNo)>0){
sam1IndSp<- grep("N",sam1$cigar)
sam2IndSp<- c()
lenRead1= unlist(lapply(sam1$cigar[sam1IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1= sam1[,"pos"]
chrRead1= sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2= c()
strRead2=c()
locRead2=c()
if(strandSpecific=="stranded"){
if(length(which(readMate==2))>0)
strRead1[which(readMate==2)]<-
as.character(revStr[which(readMate==2)])
} else if (strandSpecific=="reverse"){
strRead1[which(readMate==1)]<-
as.character(revStr[strRead1[which(readMate==1)]])
}
frqEventRead1 =lapply(sam1IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead1[tmp],length(frqEventTmpN)),
mate=rep(readMate[tmp],length(frqEventTmpN)),
chrM=rep(chrRead1[tmp],length(frqEventTmpM))))
})
frqEventRead2=NA
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[10]])))))
mateRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[11]])))))
noRead2= c()
chrRead2= c()
begRead2= c()
endRead2= c()
strRead2=c()
strAdj1<- strRead1
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec=c(as.character(strAdj1),
as.character(strAdj2))
ref=reference[which(referenceIntronExon=="exon"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"]),
strand=ref[,"strand"])
hitsAllEx <- GenomicRanges::findOverlaps(refGRanges,
readGRanges, type= "within", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
# if(length(repeatsTableToFilter)!=0){
# noRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[9]]))))
# chrRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[12]]))))
# begRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[7]]))))
# endRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[8]]))))
# noRead2M= c()
# chrRead2M= c()
# begRead2M= c()
# endRead2M= c()
#
# # analyzing reads
# noVecM=c(noRead1M,noRead2M)
# chrVecM=c(as.character(chrRead1M),
# as.character(chrRead2M))
# begVecM=c(begRead1M,begRead2M)
# endVecM=c(endRead1M,endRead2M)
#
# readGRangesM=GenomicRanges::GRanges( seqnames=chrVecM,
# IRanges::IRanges(start=begVecM, end=endVecM))
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# hitsFilter= GenomicRanges::findOverlaps(readGRangesM,
# repeatGRanges, type= "any", ignore.strand=TRUE)
# # filthitsAllExInd= which(is.na(match(S4Vectors::subjectHits(hitsBegInt),
# # S4Vectors::queryHits(hitsFilter))))
# noVecFil<- unique(noVecM[queryHits(hitsFilter)])
# filthitsAllExInd<- which(!subjectHits(hitsAllEx) %in%
# subjectHits(hitsAllEx)[
# which(noVec[subjectHits(hitsAllEx)]
# %in% noVecFil)])
# hitsAllEx=hitsAllEx[filthitsAllExInd,]
#
# }
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
if(length(S4Vectors::subjectHits(hitsAllEx))>0){
hitsApply=tapply(
noVec[S4Vectors::subjectHits(hitsAllEx)],
S4Vectors::queryHits(hitsAllEx),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
exSkipRes<- rep(0,nrow(reference))
exSkipRes[which(referenceIntronExon=="exon")]<- refRes
rm("refRes")
}
}
########!!!
########
finalRes<-c()
if(length(exExRes)==0)
exExRes<- rep(0,nrow(reference))
if(length(intRetRes)==0)
intRetRes<- rep(0,nrow(reference))
if(length(intSpanRes)==0)
intSpanRes<- rep(0,nrow(reference))
if(length(exSkipRes)==0)
exSkipRes<- rep(0,nrow(reference))
# if(length(exExRes)>0){
if("ExEx" %in% method)
finalRes<-c(finalRes, exExRes)
rm("exExRes")
# if(length(intRetRes)>0)
if("IntRet" %in% method)
finalRes<-c(finalRes, intRetRes)
rm("intRetRes")
########
########!!!
# if(length(intSpanRes)>0)
if("IntSpan" %in% method)
finalRes<-c(finalRes, intSpanRes)
rm("intSpanRes")
# if(length(exSkipRes)>0)
if("ExSkip" %in% method)
finalRes<-c(finalRes, exSkipRes)
rm("exSkipRes")
########!!!
########
if(logFile!="")
cat( "Singleend ",
qNam, " ", length(finalRes), "\n",
file=logFile, append=appendLogFile)
cat( "Singleend ",
qNam, " ", length(finalRes), "\n")
# if(is.null(finalRes) | (length(finalRes)==0))
# finalRes<- rep(0,
# length(which(method%in%c("ExEx", "IntRet", "IntSpan", "ExSkip"))))
return(finalRes)
rm("finalRes")
#End of defining function for single mapped reads that runs on parallel cores
}
gacatag/IntEREst documentation built on Aug. 20, 2023, 6:06 p.m.
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Defines functions interestIntExAnalyseSingleStranded interestIntExAnalysePairStranded
interestIntExAnalysePairStranded <- function(
readTmp,
reference,
maxNoMappedReads,
logFile,
method,
appendLogFile,
repeatsTableToFilter,
referenceIntronExon,
junctionReadsOnly,
limitRanges,
strandSpecific,
excludeFusionReads){
revStr<- c("-", "+", "*")
names(revStr)<- c("+", "-", "*")
qNam<- as.data.frame(GenomicAlignments::first(readTmp))[1,"qname"]
if(logFile!="")
cat( "start ",
qNam, "\n",
file=logFile, append=appendLogFile)
cat( "start ",
qNam, "\n")
if(length(limitRanges)>0){
readTmpFirst<- GenomicAlignments::first(readTmp)
readTmpSecond<- GenomicAlignments::second(readTmp)
if(strandSpecific=="stranded"){
GenomicRanges::strand(readTmpFirst)<-
as.character(GenomicRanges::strand(readTmpFirst))
GenomicRanges::strand(readTmpSecond)<-
revStr[as.character(GenomicRanges::strand(readTmpSecond))]
} else if (strandSpecific=="reverse"){
GenomicRanges::strand(readTmpSecond)<-
as.character(GenomicRanges::strand(readTmpSecond))
GenomicRanges::strand(readTmpFirst)<-
revStr[as.character(GenomicRanges::strand(readTmpFirst))]
}
r1Map<- GenomicRanges::findOverlaps(
readTmpFirst,
limitRanges,
type= "within",
ignore.strand= FALSE)
r2Map<- GenomicRanges::findOverlaps(
readTmpSecond,
limitRanges,
type= "within",
ignore.strand= FALSE)
filLimInd<- sort(unique(intersect(S4Vectors::queryHits(r1Map),
S4Vectors::queryHits(r2Map))),
decreasing=FALSE)
filExtra<- c()
if(excludeFusionReads){
r1LimReads<- tapply(queryHits(r1Map),subjectHits(r1Map), unique)
r2LimReads<- tapply(queryHits(r2Map),subjectHits(r2Map), unique)
commonSubjects<- intersect(names(r1LimReads), names(r2LimReads))
filExtraTmp<- lapply(commonSubjects,
function(x) return (
intersect(r1LimReads[[x]], r2LimReads[[x]])
))
filExtra<- unique(unlist(filExtraTmp))
if(length(filExtra[which(!is.na(filExtra))])>0)
filLimInd<- intersect(filLimInd, filExtra)
}
readTmp<- readTmp[filLimInd,]
}
filStrandInd<-which ( xor(
(as.data.frame(GenomicAlignments::first(readTmp))[,"strand"]=="+") ,
(as.data.frame(GenomicAlignments::second(readTmp))[,"strand"]=="+") ))
readTmp<- readTmp[filStrandInd,]
sam1<- as.data.frame(GenomicAlignments::first(readTmp))[,
c("qname", "rname", "strand", "pos", "qual", "cigar")]
sam2<- as.data.frame(GenomicAlignments::second(readTmp))[,
c("qname", "rname", "strand", "pos", "qual", "cigar")]
colnames(sam1)<- c("qName","rName","strand","pos","qual",
"cigar")
colnames(sam2)<- c("qName","rName","strand","pos","qual",
"cigar")
# if(logFile!="")
# cat( "Analyzing paired reads, ID: ", sam1[1,"qName"], "\n",
# file=logFile, append=appendLogFile)
# cat( "Analyzing paired reads, ID: ", sam1[1,"qName"], "\n")
######
######!!!
exExRes<- c()
intRetRes<- c()
intSpanRes<- c()
exSkipRes<- c()
if(length(readTmp)>0) {
if( length(which(method %in% c("IntRet","ExEx")))>0 ){
######!!!
######
lenRead1= unlist(lapply(sam1$cigar, function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
lenRead2= unlist(lapply(sam2$cigar, function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1=sam1[,"pos"]
chrRead1=sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2=sam2[,"rName"]
locRead2=sam2[,"pos"]
strRead2=sam2[,"strand"]
if(strandSpecific=="stranded"){
strAdj1<- as.character(strRead1)
strAdj2<- as.character(revStr[strRead2])
} else if (strandSpecific=="reverse"){
strAdj2<- as.character(strRead2)
strAdj1<- as.character(revStr[strRead1])
}
frqEventRead1<- lapply(1:length(sam1$cigar), function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
,split="")))]
frqEventTmp=frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
return( list(readNo=rep(tmp,length(frqEventTmpM)),
chr=rep(chrRead1[tmp],length(frqEventTmpM)),
frqEventTmpM, begEventTmpM, endEventTmpM,
str=rep(strRead1[tmp],length(frqEventTmpM))) )
})
frqEventRead2<- lapply(1:length(sam2$cigar), function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam2$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam2$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam2$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead2[tmp], locRead2[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
return(list(readNo=rep(tmp,length(frqEventTmpM)),
chr=rep(chrRead2[tmp],length(frqEventTmpM)),
frqEventTmpM, begEventTmpM, endEventTmpM,
str=rep(strRead2[tmp],length(frqEventTmpM))))
})
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[2]])))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[6]])))))
noRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[1]]))))
chrRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
as.character(unlist(tmp[[2]])))))
begRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[4]]))))
endRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[5]]))))
strRead2=as.vector(unlist(sapply(frqEventRead2, function(tmp)
as.character(unlist(tmp[[6]])))))
if(strandSpecific=="stranded"){
strAdj1<- as.character(strRead1)
strAdj2<- as.character(revStr[strRead2])
} else if (strandSpecific=="reverse"){
strAdj2<- as.character(strRead2)
strAdj1<- as.character(revStr[strRead1])
}
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec=c(as.character(strAdj1),
as.character(strAdj2))
methodNo=which(method=="ExEx")
if(length(methodNo)>0){
ref=reference[which(referenceIntronExon=="exon"),]
#if(strandSpecific%in%c("stranded","reverse")){
# FOR READ1
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1), strand=ref[,"strand"])
if(logFile!="")
cat( "Part1 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits1_1 <- GenomicRanges::findOverlaps(read1GRanges, refGRanges,
type= "start", ignore.strand=FALSE)
if(logFile!="")
cat( "Part2 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits1_2 <- GenomicRanges::findOverlaps(read1GRanges, refGRanges,
type= "end", ignore.strand=FALSE)
if(logFile!="")
cat( "Part3 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits1_3 <- GenomicRanges::findOverlaps(read1GRanges, refGRanges,
type= "equal", ignore.strand=FALSE)
if(logFile!="")
cat( "Part4 ",qNam, "\n",
file=logFile, append=appendLogFile)
# FOR READ2
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2,
end=endRead2),
strand=strAdj2)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"],
end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1),
strand=ref[,"strand"])
if(logFile!="")
cat( "Part1 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits2_1 <- GenomicRanges::findOverlaps(read2GRanges, refGRanges,
type= "start", ignore.strand=FALSE)
if(logFile!="")
cat( "Part2 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits2_2 <- GenomicRanges::findOverlaps(read2GRanges, refGRanges,
type= "end",
ignore.strand=FALSE)
if(logFile!="")
cat( "Part3 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits2_3 <- GenomicRanges::findOverlaps(read2GRanges, refGRanges,
type= "equal",
ignore.strand=FALSE)
if(logFile!="")
cat( "Part4 ",qNam, "\n",
file=logFile, append=appendLogFile)
hitsSubject<- c()
hitsQuery<- c()
hits1Subject=c()
hits1Query=c()
hits2Subject=c()
hits2Query=c()
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter= GenomicRanges::findOverlaps(read1GRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
filtInd1_1= which(is.na(match(S4Vectors::queryHits(hits1_1),
S4Vectors::queryHits(hitsFilter))))
filtInd1_2= which(is.na(match(S4Vectors::queryHits(hits1_2),
S4Vectors::queryHits(hitsFilter))))
filtInd1_3= which(is.na(match(S4Vectors::queryHits(hits1_3),
S4Vectors::queryHits(hitsFilter))))
hitsFilter= GenomicRanges::findOverlaps(read2GRanges,
repeatGRanges, type= "any",
ignore.strand=TRUE)
filtInd2_1= which(is.na(match(S4Vectors::queryHits(hits2_1),
S4Vectors::queryHits(hitsFilter))))
filtInd2_2= which(is.na(match(S4Vectors::queryHits(hits2_2),
S4Vectors::queryHits(hitsFilter))))
filtInd2_3= which(is.na(match(S4Vectors::queryHits(hits2_3),
S4Vectors::queryHits(hitsFilter))))
hits1_1= hits1_1[filtInd1_1,]
hits1_2= hits1_2[filtInd1_2,]
hits1_3= hits1_3[filtInd1_3,]
hits2_1= hits2_1[filtInd2_1,]
hits2_2= hits2_2[filtInd2_2,]
hits2_3= hits2_3[filtInd2_3,]
}
# Include the reads that completely map to exons if user asked
if(!junctionReadsOnly){
hits1Extra= GenomicRanges::findOverlaps(read1GRanges,
refGRanges, type= "within", ignore.strand=FALSE)
hits2Extra= GenomicRanges::findOverlaps(read2GRanges,
refGRanges, type= "within", ignore.strand=FALSE)
hits1Subject=S4Vectors::subjectHits(hits1Extra)
hits1Query=S4Vectors::queryHits(hits1Extra)
hits2Subject=S4Vectors::subjectHits(hits2Extra)
hits2Query=S4Vectors::queryHits(hits2Extra)
}
hits1Subject=c(hits1Subject, S4Vectors::subjectHits(hits1_1),
S4Vectors::subjectHits(hits1_2),S4Vectors::subjectHits(hits1_3))
hits2Subject=c(hits2Subject, S4Vectors::subjectHits(hits2_1),
S4Vectors::subjectHits(hits2_2),S4Vectors::subjectHits(hits2_3))
if(logFile!="")
cat( "Part5 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits1Query=c(hits1Query, S4Vectors::queryHits(hits1_1),
S4Vectors::queryHits(hits1_2), S4Vectors::queryHits(hits1_3))
hits2Query=c(hits2Query, S4Vectors::queryHits(hits2_1),
S4Vectors::queryHits(hits2_2), S4Vectors::queryHits(hits2_3))
if(logFile!="")
cat( "Part6 ",qNam, "\n",
file=logFile, append=appendLogFile)
refRes= rep(0,nrow(ref))
if(length(hits1Query)>0){
hitsApply= tapply(c(noRead1[hits1Query], noRead2[hits2Query]),
c(hits1Subject, hits2Subject),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
if(logFile!="")
cat( "Part7 ",qNam, "\n",
file=logFile, append=appendLogFile)
exExRes<-rep(0, nrow(reference))
exExRes[which(referenceIntronExon=="exon")]<- refRes
rm("refRes")
}
methodNo=which(method=="IntRet")
if((length(methodNo)>0) & (! junctionReadsOnly)){
ref=reference[which(referenceIntronExon=="intron"),]
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2, end=endRead2), strand=strAdj2)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"],
end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1),
strand=ref[,"strand"])
hits1 <- GenomicRanges::findOverlaps(read1GRanges, refGRanges,
type= "any", ignore.strand=FALSE)
hits2 <- GenomicRanges::findOverlaps(read2GRanges, refGRanges,
type= "any", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter1= GenomicRanges::findOverlaps(read1GRanges,
repeatGRanges, type= "any",ignore.strand=TRUE)
hitsFilter2= GenomicRanges::findOverlaps(read2GRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
# Explanation: If both reads have regions overlapping repeat regions ignore them!
filNoHits<-
unique(intersect(noRead1[queryHits(hitsFilter1)],
noRead2[queryHits(hitsFilter2)]))
filtInd1=
which( !(noRead1[S4Vectors::queryHits(hits1)] %in% filNoHits))
filtInd2=
which( !(noRead2[S4Vectors::queryHits(hits2)] %in% filNoHits))
hits1=hits1[filtInd1,]
hits2=hits2[filtInd2,]
}
refRes= rep(0,nrow(ref))
if(length(S4Vectors::queryHits(hits1))>0 | length(S4Vectors::queryHits(hits2))>0){
hitsApply=tapply(
c(noRead1[S4Vectors::queryHits(hits1)],
noRead2[S4Vectors::queryHits(hits2)]),
c(S4Vectors::subjectHits(hits1), S4Vectors::subjectHits(hits2)),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(unique(names(hitsApply)))]=
as.vector(hitsApply)
}
intRetRes<- rep(0,nrow(reference))
intRetRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
} else if ((length(methodNo)>0) & (junctionReadsOnly)) {
ref=reference[which(referenceIntronExon=="intron"),]
refEndGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"end"], end=ref[,"end"]),
strand=ref[,"strand"])
refBegGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"begin"]),
strand=ref[,"strand"])
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
hitsEnd1 <- GenomicRanges::findOverlaps(refEndGRanges, read1GRanges,
type= "within", ignore.strand=FALSE)
hitsBeg1 <- GenomicRanges::findOverlaps(refBegGRanges, read1GRanges,
type= "within", ignore.strand=FALSE)
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2, end=endRead2), strand=strAdj2)
hitsEnd2 <- GenomicRanges::findOverlaps(refEndGRanges, read2GRanges,
type= "within", ignore.strand=FALSE)
hitsBeg2 <- GenomicRanges::findOverlaps(refBegGRanges, read2GRanges,
type= "within", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter1= GenomicRanges::findOverlaps(read1GRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
hitsFilter2= GenomicRanges::findOverlaps(read2GRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
noFilQuHits<-
intersect(noRead1[queryHits(hitsFilter1)],
noRead2[queryHits(hitsFilter2)])
filtEndInd1= which(! noRead1[S4Vectors::subjectHits(hitsEnd1)] %in%
noFilQuHits)
filtBegInd1= which(! noRead1[S4Vectors::subjectHits(hitsBeg1)] %in%
noFilQuHits)
filtEndInd2= which(! noRead2[S4Vectors::subjectHits(hitsEnd2)] %in%
noFilQuHits)
filtBegInd2= which(! noRead2[S4Vectors::subjectHits(hitsBeg2)] %in%
noFilQuHits)
hitsEnd1=hitsEnd1[filtEndInd1,]
hitsBeg1=hitsBeg1[filtBegInd1,]
hitsEnd2=hitsEnd2[filtEndInd2,]
hitsBeg2=hitsBeg2[filtBegInd2,]
}
refRes= rep(0,nrow(ref))
refResBeg= refRes
refResEnd= refRes
if( (length(S4Vectors::subjectHits(hitsBeg1))>0) |
(length(S4Vectors::subjectHits(hitsEnd1))>0) |
(length(S4Vectors::subjectHits(hitsBeg2))>0) |
(length(S4Vectors::subjectHits(hitsEnd2))>0) ){
hitsEndApply=tapply(
c(noRead1[S4Vectors::subjectHits(hitsEnd1)],
noRead2[S4Vectors::subjectHits(hitsEnd2)]),
c(S4Vectors::queryHits(hitsEnd1), S4Vectors::queryHits(hitsEnd2)),
function(tmp) return(length(unique(tmp))) )
hitsBegApply=tapply(
c(noRead1[S4Vectors::subjectHits(hitsBeg1)],
noRead2[S4Vectors::subjectHits(hitsBeg2)]),
c(S4Vectors::queryHits(hitsBeg1), S4Vectors::queryHits(hitsBeg2)),
function(tmp) return(length(unique(tmp))) )
refResBeg[as.numeric(names(hitsBegApply))]=
as.numeric(hitsBegApply)
refResEnd[as.numeric(names(hitsEndApply))]=
as.numeric(hitsEndApply)
refRes=refResBeg+refResEnd
rm("refResBeg","refResEnd")
}
intRetRes<- rep(0,nrow(reference))
intRetRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
}
########
########!!!
}
methodNo=which(method=="IntSpan")
if(length(methodNo)>0){
sam1IndSp<- grep("N",sam1$cigar)
sam2IndSp<- grep("N",sam2$cigar)
lenRead1= unlist(lapply(sam1$cigar[sam1IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
lenRead2= unlist(lapply(sam2$cigar[sam2IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1=sam1[,"pos"]
chrRead1=sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2=sam2[,"rName"]
locRead2=sam2[,"pos"]
strRead2=sam2[,"strand"]
frqEventRead1 =lapply(sam1IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead1[tmp],length(frqEventTmpN)) ))
})
frqEventRead2= lapply(sam2IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam2$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam2$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam2$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead2[tmp], locRead2[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead2[tmp],length(frqEventTmpN) )))
})
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[10]])))))
noRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[1]]))))
chrRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[2]]))))
begRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[4]]))))
endRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[5]]))))
strRead2=as.vector(unlist(sapply(frqEventRead2, function(tmp)
as.character(unlist(tmp[[10]])))))
if(strandSpecific=="stranded"){
strAdj1<- as.character(strRead1)
strAdj2<- as.character(revStr[strRead2])
} else if (strandSpecific=="reverse"){
strAdj2<- as.character(strRead2)
strAdj1<- as.character(revStr[strRead1])
}
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec<- c(strAdj1,strAdj2)
ref=reference[which(referenceIntronExon=="intron"),]
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2, end=endRead2), strand=strAdj2)
# refIntBegGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
# IRanges::IRanges(start=ref[,"begin"]-1, end=ref[,"begin"]-1),
# strand=ref[,"strand"])
# refIntEndGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
# IRanges::IRanges(start=ref[,"end"]+1, end=ref[,"end"]+1),
# strand=ref[,"strand"])
refIntGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"]),
strand=ref[,"strand"])
### !!!
### THIS IS NOT THE BEST WAY. WHY SEPARATE ON BEGIN AND END ?
###WHY NOT hitsBegInt <- GenomicRanges::findOverlaps(readGRanges,
### refIntGRanges, type= "equal")
# hitsBegInt1 <- GenomicRanges::findOverlaps(read1GRanges,
# refIntBegGRanges, type= "end", ignore.strand=FALSE)
# hitsEndInt1 <- GenomicRanges::findOverlaps(read1GRanges,
# refIntEndGRanges, type= "start", ignore.strand=FALSE)
# hitsBegInt2 <- GenomicRanges::findOverlaps(read2GRanges,
# refIntBegGRanges, type= "end", ignore.strand=FALSE)
# hitsEndInt2 <- GenomicRanges::findOverlaps(read2GRanges,
# refIntEndGRanges, type= "start", ignore.strand=FALSE)
hitsInt1 <- GenomicRanges::findOverlaps(read1GRanges,
refIntGRanges, type= "equal", ignore.strand=FALSE)
hitsInt2 <- GenomicRanges::findOverlaps(read2GRanges,
refIntGRanges, type= "equal", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
# if(length(repeatsTableToFilter)!=0){
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# hitsFilter1= GenomicRanges::findOverlaps(read1GRanges,
# repeatGRanges, type= "any", ignore.strand=TRUE)
# hitsFilter2= GenomicRanges::findOverlaps(read2GRanges,
# repeatGRanges, type= "any", ignore.strand=TRUE)
#
# noFilQuHits<-
# intersect(noRead1[queryHits(hitsFilter1)],
# noRead2[queryHits(hitsFilter2)])
#
# filtEndInd1= which(! noRead1[S4Vectors::subjectHits(hitsEndInt1)] %in%
# noFilQuHits)
# filtBegInd1= which(! noRead1[S4Vectors::subjectHits(hitsBegInt1)] %in%
# noFilQuHits)
#
# filtEndInd2= which(! noRead2[S4Vectors::subjectHits(hitsEndInt2)] %in%
# noFilQuHits)
# filtBegInd2= which(! noRead2[S4Vectors::subjectHits(hitsBegInt2)] %in%
# noFilQuHits)
#
#
# hitsBegInt1=hitsBegInt1[filtBegInd1,]
# hitsEndInt1=hitsEndInt1[filtEndInd1,]
# hitsBegInt2=hitsBegInt2[filtBegInd2,]
# hitsEndInt2=hitsEndInt2[filtEndInd2,]
# }
# if(length(repeatsTableToFilter)!=0){
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# hitsFilter1= GenomicRanges::findOverlaps(read1GRanges,
# repeatGRanges, type= "equal", ignore.strand=TRUE)
# hitsFilter2= GenomicRanges::findOverlaps(read2GRanges,
# repeatGRanges, type= "equal", ignore.strand=TRUE)
#
# noFilQuHits<-
# intersect(noRead1[queryHits(hitsFilter1)],
# noRead2[queryHits(hitsFilter2)])
#
# filtInd1= which(! noRead1[S4Vectors::subjectHits(hitsInt1)] %in%
# noFilQuHits)
#
# filtEndInd2= which(! noRead2[S4Vectors::subjectHits(hitsInt2)] %in%
# noFilQuHits)
#
# hitsInt1=hitsInt1[filtInd1,]
# hitsInt2=hitsInt2[filtInd2,]
# }
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
# if(length(c(S4Vectors::queryHits(hitsBegInt1),
# S4Vectors::queryHits(hitsEndInt1)))>0 |
# length(c(S4Vectors::queryHits(hitsBegInt2),
# S4Vectors::queryHits(hitsEndInt2)))>0){
# hitsApply=tapply(
# c(noRead1[c(S4Vectors::queryHits(hitsBegInt1),
# S4Vectors::queryHits(hitsEndInt1))],
# noRead2[c(S4Vectors::queryHits(hitsBegInt2),
# S4Vectors::queryHits(hitsEndInt2))]),
# c(S4Vectors::subjectHits(hitsBegInt1),
# S4Vectors::subjectHits(hitsEndInt1),
# S4Vectors::subjectHits(hitsBegInt2),
# S4Vectors::subjectHits(hitsEndInt2)),
# function(tmp) return(length(unique(tmp))) )
# refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
# }
if(length(S4Vectors::queryHits(hitsInt1))>0 |
length(S4Vectors::queryHits(hitsInt2))>0){
hitsApply=tapply(
c(noRead1[S4Vectors::queryHits(hitsInt1)],
noRead2[S4Vectors::queryHits(hitsInt2)]),
c(S4Vectors::subjectHits(hitsInt1),
S4Vectors::subjectHits(hitsInt2)),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
intSpanRes<- rep(0,nrow(reference))
intSpanRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
}
####
### NEW ExSkip
methodNo=which(method=="ExSkip")
if(length(methodNo)>0){
sam1IndSp<- grep("N",sam1$cigar)
sam2IndSp<- grep("N",sam2$cigar)
lenRead1= unlist(lapply(sam1$cigar[sam1IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
lenRead2= unlist(lapply(sam2$cigar[sam2IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1=sam1[,"pos"]
chrRead1=sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2=sam2[,"rName"]
locRead2=sam2[,"pos"]
strRead2=sam2[,"strand"]
frqEventRead1 =lapply(sam1IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead1[tmp],length(frqEventTmpN)) ))
})
frqEventRead2= lapply(sam2IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam2$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam2$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam2$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead2[tmp], locRead2[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead2[tmp],length(frqEventTmpN) )))
})
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[10]])))))
noRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[1]]))))
chrRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[2]]))))
begRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[4]]))))
endRead2= as.vector(unlist(sapply(frqEventRead2, function(tmp)
unlist(tmp[[5]]))))
strRead2=as.vector(unlist(sapply(frqEventRead2, function(tmp)
as.character(unlist(tmp[[10]])))))
if(strandSpecific=="stranded"){
strAdj1<- as.character(strRead1)
strAdj2<- as.character(revStr[strRead2])
} else if (strandSpecific=="reverse"){
strAdj2<- as.character(strRead2)
strAdj1<- as.character(revStr[strRead1])
}
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec<- c(strAdj1,strAdj2)
ref=reference[which(referenceIntronExon=="exon"),]
read1GRanges=GenomicRanges::GRanges( seqnames=chrRead1,
IRanges::IRanges(start=begRead1, end=endRead1), strand=strAdj1)
read2GRanges=GenomicRanges::GRanges( seqnames=chrRead2,
IRanges::IRanges(start=begRead2, end=endRead2), strand=strAdj2)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"]),
strand=ref[,"strand"])
hitsAllEx1 <- GenomicRanges::findOverlaps(refGRanges,
read1GRanges, type= "within",
ignore.strand= FALSE)
hitsAllEx2 <- GenomicRanges::findOverlaps(refGRanges,
read2GRanges, type= "within",
ignore.strand= FALSE)
# Filter reads mapped to repeats regions if requested
# if(length(repeatsTableToFilter)!=0){
# noRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[9]]))))
# chrRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[2]]))))
# begRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[7]]))))
# endRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[8]]))))
#
# noRead2M= as.vector(unlist(sapply(frqEventRead2, function(tmp)
# unlist(tmp[[9]]))))
# chrRead2M= as.vector(unlist(sapply(frqEventRead2, function(tmp)
# unlist(tmp[[2]]))))
# begRead2M= as.vector(unlist(sapply(frqEventRead2, function(tmp)
# unlist(tmp[[7]]))))
# endRead2M= as.vector(unlist(sapply(frqEventRead2, function(tmp)
# unlist(tmp[[8]]))))
#
# # analyzing reads
# noVecM=c(noRead1M,noRead2M)
# chrVecM=c(as.character(chrRead1M),
# as.character(chrRead2M))
# begVecM=c(begRead1M,begRead2M)
# endVecM=c(endRead1M,endRead2M)
#
# readGRangesM1=GenomicRanges::GRanges( seqnames=chrRead1M,
# IRanges::IRanges(start=begRead1M, end=endRead1M))
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# hitsFilter1= GenomicRanges::findOverlaps(readGRangesM1,
# repeatGRanges, type= "any", ignore.strand=TRUE)
# hitsFilter2= GenomicRanges::findOverlaps(readGRangesM2,
# repeatGRanges, type= "any", ignore.strand=TRUE)
#
# # noVecFil<- unique(noVecM[queryHits(hitsFilter)])
# # filthitsAllExInd<- which(!subjectHits(hitsAllEx) %in%
# # subjectHits(hitsAllEx)[
# # which(noVec[subjectHits(hitsAllEx)]
# # %in% noVecFil)])
# # hitsAllEx=hitsAllEx[filthitsAllExInd,]
# noFilQuHits<-
# intersect(noRead1[queryHits(hitsFilter1)],
# noRead2[queryHits(hitsFilter2)])
#
# filtAllInd1= which(! noRead1[S4Vectors::subjectHits(hitsAllEx1)] %in%
# noFilQuHits)
# filtAllInd2= which(! noRead1[S4Vectors::subjectHits(hitsAllEx2)] %in%
# noFilQuHits)
#
#
#
# hitsAllEx1=hitsAllEx1[filtAllInd1,]
# hitsAllEx2=hitsAllEx2[filtAllInd2,]
# # hitsBegInt2=hitsBegInt2[filtBegInd2,]
# # hitsEndInt2=hitsEndInt2[filtEndInd2,]
#
# }
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
if(length(c(S4Vectors::subjectHits(hitsAllEx1),
S4Vectors::subjectHits(hitsAllEx2)))>0){
hitsApply=tapply(
c(noRead1[S4Vectors::subjectHits(hitsAllEx1)],
noRead2[S4Vectors::subjectHits(hitsAllEx2)]),
c(S4Vectors::queryHits(hitsAllEx1),
S4Vectors::queryHits(hitsAllEx2)),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
exSkipRes<- rep(0,nrow(reference))
exSkipRes[which(referenceIntronExon=="exon")]<- refRes
rm("refRes")
}
}
########!!!
########
########!!!
########
finalRes<-c()
if(length(exExRes)==0)
exExRes<- rep(0,nrow(reference))
if(length(intRetRes)==0)
intRetRes<- rep(0,nrow(reference))
if(length(intSpanRes)==0)
intSpanRes<- rep(0,nrow(reference))
if(length(exSkipRes)==0)
exSkipRes<- rep(0,nrow(reference))
# if(length(exExRes)>0){
if("ExEx" %in% method)
finalRes<-c(finalRes, exExRes)
rm("exExRes")
# if(length(intRetRes)>0)
if("IntRet" %in% method)
finalRes<-c(finalRes, intRetRes)
rm("intRetRes")
########
########!!!
# if(length(intSpanRes)>0)
if("IntSpan" %in% method)
finalRes<-c(finalRes, intSpanRes)
rm("intSpanRes")
# if(length(exSkipRes)>0)
if("ExSkip" %in% method)
finalRes<-c(finalRes, exSkipRes)
rm("exSkipRes")
########!!!
########
if(logFile!="")
cat( "end ",
qNam, " ", length(finalRes), "\n",
file=logFile, append=appendLogFile)
cat( "end ",
qNam, " ", length(finalRes), "\n")
# if(is.null(finalRes))
# finalRes<- rep(0,
# length(which(method%in%c("ExEx", "IntRet", "IntSpan", "ExSkip"))))
return(finalRes)
rm("finalRes")
#End of defining function for paired-mapped reads that runs on parallel cores
}
# For single reads
interestIntExAnalyseSingleStranded <- function(
readTmp,
reference,
maxNoMappedReads,
logFile,
method,
appendLogFile,
repeatsTableToFilter,
referenceIntronExon,
junctionReadsOnly,
limitRanges,
strandSpecific,
excludeFusionReads)
{
revStr<- c("-", "+", "*")
names(revStr)<- c("+", "-", "*")
qNam<- as.data.frame(readTmp)[1, "qname"]
if(logFile!="")
cat( "Singlestart ",
qNam, "\n",
file=logFile, append=appendLogFile)
cat( "Singlestart ",
qNam, "\n")
# Filtering readTmp based on number of mapping targets for each read
lenTmp<- unlist(sapply(readTmp, length))
readTmpFil<- readTmp[which(lenTmp<= maxNoMappedReads)]
sam2= NA
sam1Flag<- mcols(unlist(readTmpFil))$flag
sam1FlagMat<-bamFlagAsBitMatrix(sam1Flag)
readMate<- rep(1,nrow(sam1FlagMat))
readMate[which(sam1FlagMat[,"isSecondMateRead"]==1)]<- 2
readTmpFirst<- unlist(readTmpFil)
if(strandSpecific=="stranded"){
if(length(which(readMate==1))>0)
GenomicRanges::strand(readTmpFirst)[which(readMate==1)]<-
as.character(GenomicRanges::strand(readTmpFirst)[which(readMate==1)])
if(length(which(readMate==2))>0)
GenomicRanges::strand(readTmpFirst)[which(readMate==2)]<-
as.character(revStr[as.character(GenomicRanges::strand(readTmpFirst))][which(readMate==2)])
} else if (strandSpecific=="reverse"){
if(length(which(readMate==2))>0)
GenomicRanges::strand(readTmpFirst)[which(readMate==2)]<-
as.character(GenomicRanges::strand(readTmpFirst)[which(readMate==2)])
if(length(which(readMate==1))>0)
GenomicRanges::strand(readTmpFirst)[which(readMate==1)]<-
as.character(revStr[as.character(GenomicRanges::strand(readTmpFirst))][which(readMate==1)])
}
if(length(limitRanges)>0 & length(readTmpFirst)>0){
r1Map<- GenomicRanges::findOverlaps(
readTmpFirst,
limitRanges,
type= "within",
ignore.strand= FALSE)
filLimInd<- sort(unique(S4Vectors::queryHits(r1Map)), decreasing=FALSE)
readTmpFirst<- readTmpFirst[filLimInd,]
}
#Extract information of the mapped pieces of the reads
sam1<- as.data.frame(readTmpFirst)[, c("qname", "rname", "strand",
"pos", "qual", "cigar")]
colnames(sam1)<- c("qName","rName","strand","pos","qual",
"cigar")
### Incorporate FLAGS to figure what reads are fisrt or second from mate in singletons
### then adjust strands accordingly.
### Use flags<-bamFlagAsBitMatrix(mcols(unlist(readTmpFil))$flag)
### Column 7 and 8 is first or second mate
### Update what in scanbamwhat with scParam3=Rsamtools::ScanBamParam(
###what=Rsamtools::scanBamWhat()[c(1,
### 3,5,8,13,9, 10, 6, 4, 14, 15, 2)],
# if(logFile!="")
# cat( "Analyzing single reads, ID: ", sam1[1,"qName"], "\n",
# file=logFile, append=appendLogFile)
# cat( "Analyzing single reads, ID: ", sam1[1,"qName"], "\n")
######
######!!!
exExRes<- c()
intRetRes<- c()
intSpanRes<- c()
exSkipRes<- c()
if(length(readTmp)>0){
if( length(which(method %in% c("IntRet","ExEx")))>0 ){
######!!!
######
lenRead1= unlist(lapply(sam1$cigar, function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
lenRead2= 0
locRead1= sam1[,"pos"]
chrRead1= sam1[,"rName"]
chrRead2= 0
locRead2= 0
strRead1=sam1[,"strand"]
strRead2=0
if(strandSpecific=="stranded"){
if(length(which(readMate==2))>0)
strRead1[which(readMate==2)]<-
as.character(revStr[which(readMate==2)])
} else if (strandSpecific=="reverse"){
strRead1[which(readMate==1)]<-
as.character(revStr[strRead1[which(readMate==1)]])
}
frqEventRead1 =lapply(1:length(sam1$cigar), function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
return( list(readNo=rep(tmp,length(frqEventTmpM)),
chr=rep(chrRead1[tmp],length(frqEventTmpM)),
frqEventTmpM, begEventTmpM, endEventTmpM,
strand=rep(strRead1[tmp],length(frqEventTmpM)),
mate=rep(readMate[tmp],length(frqEventTmpM))))
})
frqEventRead2=NA
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[6]])))))
mateRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[7]])))))
noRead2= c()
chrRead2= c()
begRead2= c()
endRead2= c()
strRead2= c()
strRead2= c()
strAdj1<- strRead1
##### HERE 1 !!!!
strAdj2<- c()
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec=c(as.character(strAdj1),
as.character(strAdj2))
exExRes<- c()
intRetRes<- c()
methodNo= which(method=="ExEx")
if(length(methodNo)>0){
ref= reference[which(referenceIntronExon=="exon"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1), strand=ref[,"strand"])
hits1 <- GenomicRanges::findOverlaps(readGRanges, refGRanges,
type= "start", ignore.strand=FALSE)
if(logFile!="")
cat( "Part8 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits2 <- GenomicRanges::findOverlaps(readGRanges, refGRanges,
type= "end", ignore.strand=FALSE)
if(logFile!="")
cat( "Part9 ",qNam, "\n",
file=logFile, append=appendLogFile)
hits3 <- GenomicRanges::findOverlaps(readGRanges, refGRanges,
type= "equal", ignore.strand=FALSE)
if(logFile!="")
cat( "Part10 ",qNam, "\n",
file=logFile, append=appendLogFile)
hitsSubject<- c()
hitsQuery<- c()
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter= GenomicRanges::findOverlaps(readGRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
filtInd1= which(is.na(match(S4Vectors::queryHits(hits1),
S4Vectors::queryHits(hitsFilter))))
filtInd2= which(is.na(match(S4Vectors::queryHits(hits2),
S4Vectors::queryHits(hitsFilter))))
filtInd3= which(is.na(match(S4Vectors::queryHits(hits3),
S4Vectors::queryHits(hitsFilter))))
hits1= hits1[filtInd1,]
hits2= hits2[filtInd2,]
hits3= hits3[filtInd3,]
}
# Include the reads that completely map to exons if user asked
if(!junctionReadsOnly){
hitsExtra= GenomicRanges::findOverlaps(readGRanges,
refGRanges, type= "within", ignore.strand=FALSE)
hitsSubject=S4Vectors::subjectHits(hitsExtra)
hitsQuery=S4Vectors::queryHits(hitsExtra)
}
hitsSubject=c(hitsSubject, S4Vectors::subjectHits(hits1),
S4Vectors::subjectHits(hits2),S4Vectors::subjectHits(hits3))
if(logFile!="")
cat( "Part11 ",qNam, "\n",
file=logFile, append=appendLogFile)
hitsQuery=c(hitsQuery, S4Vectors::queryHits(hits1),
S4Vectors::queryHits(hits2), S4Vectors::queryHits(hits3))
refRes= rep(0,nrow(ref))
if(length(hitsQuery)>0){
hitsApply= tapply(noVec[hitsQuery], hitsSubject, function(tmp)
return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
if(logFile!="")
cat( "Part12 ",qNam, "\n",
file=logFile, append=appendLogFile)
exExRes<-rep(0, nrow(reference))
exExRes[which(referenceIntronExon=="exon")]<- refRes
rm("refRes")
}
methodNo=which(method=="IntRet")
if((length(methodNo)>0) & (! junctionReadsOnly)){
ref=reference[which(referenceIntronExon=="intron"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges(start=ref[,"begin"], end=ref[,"end"],
width=ref[,"end"]-ref[,"begin"]+1), strand=ref[,"strand"])
hits <- GenomicRanges::findOverlaps(readGRanges, refGRanges,
type= "any", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter= GenomicRanges::findOverlaps(readGRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
filtInd= which(is.na(match(S4Vectors::queryHits(hits),
S4Vectors::queryHits(hitsFilter))))
hits=hits[filtInd,]
}
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
if(length(S4Vectors::queryHits(hits))>0){
hitsApply=tapply(noVec[S4Vectors::queryHits(hits)],
S4Vectors::subjectHits(hits),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
intRetRes<- rep(0,nrow(reference))
intRetRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
} else if ((length(methodNo)>0) & (junctionReadsOnly)) {
ref=reference[which(referenceIntronExon=="intron"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
refEndGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"end"], end=ref[,"end"]),
strand=ref[,"strand"])
refBegGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"begin"]),
strand=ref[,"strand"])
hitsEnd <- GenomicRanges::findOverlaps(refEndGRanges, readGRanges,
type= "within", ignore.strand=FALSE)
hitsBeg <- GenomicRanges::findOverlaps(refBegGRanges, readGRanges,
type= "within", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
if(length(repeatsTableToFilter)!=0){
repeatGRanges= GenomicRanges::GRanges(
seqnames=repeatsTableToFilter[,"chr"],
IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
end=repeatsTableToFilter[,"end"],
width=repeatsTableToFilter[,"end"]-
repeatsTableToFilter[,"begin"]+1))
hitsFilter= GenomicRanges::findOverlaps(readGRanges,
repeatGRanges, type= "any", ignore.strand=TRUE)
filtEndInd= which(is.na(match(S4Vectors::subjectHits(hitsEnd),
S4Vectors::queryHits(hitsFilter))))
filtBegInd= which(is.na(match(S4Vectors::subjectHits(hitsBeg),
S4Vectors::queryHits(hitsFilter))))
hitsEnd=hitsEnd[filtEndInd,]
hitsBeg=hitsBeg[filtBegInd,]
}
refRes= rep(0,nrow(ref))
refResBeg= refRes
refResEnd= refRes
if( (length(S4Vectors::subjectHits(hitsBeg))>0) |
(length(S4Vectors::subjectHits(hitsEnd))>0) ){
hitsEndApply=tapply(noVec[S4Vectors::subjectHits(hitsEnd)],
S4Vectors::queryHits(hitsEnd),
function(tmp) return(length(unique(tmp))) )
hitsBegApply=tapply(noVec[S4Vectors::subjectHits(hitsBeg)],
S4Vectors::queryHits(hitsBeg),
function(tmp) return(length(unique(tmp))) )
refResBeg[as.numeric(names(hitsBegApply))]=
as.numeric(hitsBegApply)
refResEnd[as.numeric(names(hitsEndApply))]=
as.numeric(hitsEndApply)
refRes=refResBeg+refResEnd
rm("refResBeg","refResEnd")
}
intRetRes<- rep(0,nrow(reference))
intRetRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
}
}
### HERE !!!
methodNo=which(method=="IntSpan")
if(length(methodNo)>0){
sam1IndSp<- grep("N",sam1$cigar)
sam2IndSp<- c()
lenRead1= unlist(lapply(sam1$cigar[sam1IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1= sam1[,"pos"]
chrRead1= sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2= c()
strRead2=c()
locRead2=c()
if(strandSpecific=="stranded"){
if(length(which(readMate==2))>0)
strRead1[which(readMate==2)]<-
as.character(revStr[which(readMate==2)])
} else if (strandSpecific=="reverse"){
strRead1[which(readMate==1)]<-
as.character(revStr[strRead1[which(readMate==1)]])
}
frqEventRead1 =lapply(sam1IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead1[tmp],length(frqEventTmpN)),
mate=rep(readMate[tmp],length(frqEventTmpN)),
chrM=rep(chrRead1[tmp],length(frqEventTmpM))))
})
frqEventRead2=NA
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[10]])))))
mateRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[11]])))))
noRead2= c()
chrRead2= c()
begRead2= c()
endRead2= c()
strRead2=c()
strAdj1<- strRead1
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec=c(as.character(strAdj1),
as.character(strAdj2))
ref=reference[which(referenceIntronExon=="intron"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
# refIntBegGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
# IRanges::IRanges(start=ref[,"begin"]-1, end=ref[,"begin"]-1),
# strand=ref[,"strand"])
# refIntEndGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
# IRanges::IRanges(start=ref[,"end"]+1, end=ref[,"end"]+1),
# strand=ref[,"strand"])
refIntGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"]),
strand=ref[,"strand"])
### !!!
### THIS IS NOT THE BEST WAY. WHY SEPARATE ON BEGIN AND END ?
###WHY NOT hitsBegInt <- GenomicRanges::findOverlaps(readGRanges,
### refIntGRanges, type= "equal")
# hitsBegInt <- GenomicRanges::findOverlaps(readGRanges,
# refIntBegGRanges, type= "end", ignore.strand=FALSE)
# hitsEndInt <- GenomicRanges::findOverlaps(readGRanges,
# refIntEndGRanges, type= "start", ignore.strand=FALSE)
hitsInt <- GenomicRanges::findOverlaps(readGRanges,
refIntGRanges, type= "equal", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
# if(length(repeatsTableToFilter)!=0){
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# # hitsFilter= GenomicRanges::findOverlaps(readGRanges,
# # repeatGRanges, type= "any", ignore.strand=TRUE)
# # filtBegInd= which(is.na(match(S4Vectors::queryHits(hitsBegInt),
# # S4Vectors::queryHits(hitsFilter))))
# # hitsBegInt=hitsBegInt[filtBegInd,]
# # filtEndInd= which(is.na(match(S4Vectors::queryHits(hitsEndInt),
# # S4Vectors::queryHits(hitsFilter))))
# # hitsEndInt=hitsEndInt[filtEndInd,]
# hitsFilter= GenomicRanges::findOverlaps(readGRanges,
# repeatGRanges, type= "equal", ignore.strand=TRUE)
# filtInd= which(is.na(match(S4Vectors::queryHits(hitsInt),
# S4Vectors::queryHits(hitsFilter))))
# hitsInt=hitsInt[filtInd,]
# }
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
# if(length(c(S4Vectors::queryHits(hitsBegInt),
# S4Vectors::queryHits(hitsEndInt)))>0){
# hitsApply=tapply(
# noVec[c(S4Vectors::queryHits(hitsBegInt),
# S4Vectors::queryHits(hitsEndInt))],
# c(S4Vectors::subjectHits(hitsBegInt),
# S4Vectors::subjectHits(hitsEndInt)),
# function(tmp) return(length(unique(tmp))) )
# refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
# }
if(length(S4Vectors::queryHits(hitsInt))>0){
hitsApply=tapply(
noVec[S4Vectors::queryHits(hitsInt)],
c(S4Vectors::subjectHits(hitsInt)),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
intSpanRes<- rep(0,nrow(reference))
intSpanRes[which(referenceIntronExon=="intron")]<- refRes
rm("refRes")
}
####
### NEW ExSkip
methodNo=which(method=="ExSkip")
if(length(methodNo)>0){
sam1IndSp<- grep("N",sam1$cigar)
sam2IndSp<- c()
lenRead1= unlist(lapply(sam1$cigar[sam1IndSp], function(tmp) {
frqEvent=as.numeric(unlist(strsplit(tmp,split="[A-Z]")))
names(frqEvent)=unlist(strsplit(tmp,split=""))[grep('[A-Z]',
unlist(strsplit(tmp,split="")))]
return(sum(frqEvent[grep("[N|M|D]",names(frqEvent))]))
}))
locRead1= sam1[,"pos"]
chrRead1= sam1[,"rName"]
strRead1=sam1[,"strand"]
chrRead2= c()
strRead2=c()
locRead2=c()
if(strandSpecific=="stranded"){
if(length(which(readMate==2))>0)
strRead1[which(readMate==2)]<-
as.character(revStr[which(readMate==2)])
} else if (strandSpecific=="reverse"){
strRead1[which(readMate==1)]<-
as.character(revStr[strRead1[which(readMate==1)]])
}
frqEventRead1 =lapply(sam1IndSp, function (tmp) {
frqEventTmp= as.numeric(unlist(strsplit(sam1$cigar[tmp],
split="[A-Z]")))
names(frqEventTmp)= unlist(strsplit(sam1$cigar[tmp],
split=""))[grep('[A-Z]', unlist(strsplit(sam1$cigar[tmp]
, split="")))]
frqEventTmp= frqEventTmp[!is.na(match(names(frqEventTmp),
c("N","D","M")))]
# Finding start and end of the mapped pieces of the reads using cigar
eventTmp<- c(locRead1[tmp], locRead1[tmp]+
cumsum(as.numeric(frqEventTmp)))
begEventTmp<-eventTmp[-length(eventTmp)]
endEventTmp<- begEventTmp+as.numeric(frqEventTmp)-1
frqEventTmpM=frqEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
begEventTmpM=begEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
endEventTmpM=endEventTmp[!is.na(match(names(frqEventTmp),
"M"))]
frqEventTmpN=frqEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
begEventTmpN=begEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
endEventTmpN=endEventTmp[!is.na(match(names(frqEventTmp),
"N"))]
return( list(readNo=rep(tmp,length(frqEventTmpN)),
chr=rep(chrRead1[tmp],length(frqEventTmpN)),
frqEventTmpN, begEventTmpN, endEventTmpN,
frqEventTmpM, begEventTmpM, endEventTmpM,
readNoM=rep(tmp,length(frqEventTmpM)),
strand=rep(strRead1[tmp],length(frqEventTmpN)),
mate=rep(readMate[tmp],length(frqEventTmpN)),
chrM=rep(chrRead1[tmp],length(frqEventTmpM))))
})
frqEventRead2=NA
noRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[1]]))))
chrRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[2]]))))
begRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[4]]))))
endRead1= as.vector(unlist(sapply(frqEventRead1, function(tmp)
unlist(tmp[[5]]))))
strRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[10]])))))
mateRead1=as.vector(unlist(sapply(frqEventRead1, function(tmp)
as.character(unlist(tmp[[11]])))))
noRead2= c()
chrRead2= c()
begRead2= c()
endRead2= c()
strRead2=c()
strAdj1<- strRead1
# analyzing reads
noVec=c(noRead1,noRead2)
chrVec=c(as.character(chrRead1),
as.character(chrRead2))
begVec=c(begRead1,begRead2)
endVec=c(endRead1,endRead2)
strVec=c(as.character(strAdj1),
as.character(strAdj2))
ref=reference[which(referenceIntronExon=="exon"),]
readGRanges=GenomicRanges::GRanges( seqnames=chrVec,
IRanges::IRanges(start=begVec, end=endVec), strand=strVec)
refGRanges= GenomicRanges::GRanges( seqnames=ref[,"chr"],
IRanges::IRanges(start=ref[,"begin"], end=ref[,"end"]),
strand=ref[,"strand"])
hitsAllEx <- GenomicRanges::findOverlaps(refGRanges,
readGRanges, type= "within", ignore.strand=FALSE)
# Filter reads mapped to repeats regions if requested
# if(length(repeatsTableToFilter)!=0){
# noRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[9]]))))
# chrRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[12]]))))
# begRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[7]]))))
# endRead1M= as.vector(unlist(sapply(frqEventRead1, function(tmp)
# unlist(tmp[[8]]))))
# noRead2M= c()
# chrRead2M= c()
# begRead2M= c()
# endRead2M= c()
#
# # analyzing reads
# noVecM=c(noRead1M,noRead2M)
# chrVecM=c(as.character(chrRead1M),
# as.character(chrRead2M))
# begVecM=c(begRead1M,begRead2M)
# endVecM=c(endRead1M,endRead2M)
#
# readGRangesM=GenomicRanges::GRanges( seqnames=chrVecM,
# IRanges::IRanges(start=begVecM, end=endVecM))
# repeatGRanges= GenomicRanges::GRanges(
# seqnames=repeatsTableToFilter[,"chr"],
# IRanges::IRanges(start=repeatsTableToFilter[,"begin"],
# end=repeatsTableToFilter[,"end"],
# width=repeatsTableToFilter[,"end"]-
# repeatsTableToFilter[,"begin"]+1))
# hitsFilter= GenomicRanges::findOverlaps(readGRangesM,
# repeatGRanges, type= "any", ignore.strand=TRUE)
# # filthitsAllExInd= which(is.na(match(S4Vectors::subjectHits(hitsBegInt),
# # S4Vectors::queryHits(hitsFilter))))
# noVecFil<- unique(noVecM[queryHits(hitsFilter)])
# filthitsAllExInd<- which(!subjectHits(hitsAllEx) %in%
# subjectHits(hitsAllEx)[
# which(noVec[subjectHits(hitsAllEx)]
# %in% noVecFil)])
# hitsAllEx=hitsAllEx[filthitsAllExInd,]
#
# }
# Filter reads mapped completely to Either introns or exons
refRes= rep(0,nrow(ref))
if(length(S4Vectors::subjectHits(hitsAllEx))>0){
hitsApply=tapply(
noVec[S4Vectors::subjectHits(hitsAllEx)],
S4Vectors::queryHits(hitsAllEx),
function(tmp) return(length(unique(tmp))) )
refRes[as.numeric(names(hitsApply))]= as.vector(hitsApply)
}
exSkipRes<- rep(0,nrow(reference))
exSkipRes[which(referenceIntronExon=="exon")]<- refRes
rm("refRes")
}
}
########!!!
########
finalRes<-c()
if(length(exExRes)==0)
exExRes<- rep(0,nrow(reference))
if(length(intRetRes)==0)
intRetRes<- rep(0,nrow(reference))
if(length(intSpanRes)==0)
intSpanRes<- rep(0,nrow(reference))
if(length(exSkipRes)==0)
exSkipRes<- rep(0,nrow(reference))
# if(length(exExRes)>0){
if("ExEx" %in% method)
finalRes<-c(finalRes, exExRes)
rm("exExRes")
# if(length(intRetRes)>0)
if("IntRet" %in% method)
finalRes<-c(finalRes, intRetRes)
rm("intRetRes")
########
########!!!
# if(length(intSpanRes)>0)
if("IntSpan" %in% method)
finalRes<-c(finalRes, intSpanRes)
rm("intSpanRes")
# if(length(exSkipRes)>0)
if("ExSkip" %in% method)
finalRes<-c(finalRes, exSkipRes)
rm("exSkipRes")
########!!!
########
if(logFile!="")
cat( "Singleend ",
qNam, " ", length(finalRes), "\n",
file=logFile, append=appendLogFile)
cat( "Singleend ",
qNam, " ", length(finalRes), "\n")
# if(is.null(finalRes) | (length(finalRes)==0))
# finalRes<- rep(0,
# length(which(method%in%c("ExEx", "IntRet", "IntSpan", "ExSkip"))))
return(finalRes)
rm("finalRes")
#End of defining function for single mapped reads that runs on parallel cores
}
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