SplicingReads: Count a junction and paired-end reads

In IMAS: Integrative analysis of Multi-omics data for Alternative Splicing

Description

This function counts the reads that are mapped to two separate exons, mapped to either splice site of two exons (called junction reads) or within each of two exons (paired end reads).

Usage

    SplicingReads(bamfile=NULL,test.exon=NULL,spli.jun=NULL,e.ran=NULL,
        SNPchr=NULL,readsinfo="paired",inse=40)

Arguments

bamfile	A path of mapped bamfile.
test.exon	A data frame containing an alternative target exon and their neighboring exons.
spli.jun	A data frame containing spliced junction information.
e.ran	A range for parsing reads from a bamfile.
SNPchr	A chromosome number
readsinfo	Information of RNA-seq types (single- or paired- end reads).
inse	An insert size

Value

This function returns the list object providing counts the reads that are mapped to two separate exons, mapped to either splice site of two exons (called junction reads) or within each of two exons (paired end reads).

Author(s)

Seonggyun Han, Younghee Lee

Examples

    data(bamfilestest)
    ext.dir <- system.file("extdata", package="IMAS")
    samplebamfiles[,"path"] <- paste(ext.dir,"/samplebam/",samplebamfiles[,"path"],".bam",sep="")
    sampleDB <- system.file("extdata", "sampleDB", package="IMAS")
    transdb <- loadDb(sampleDB)
    ## Not run: 
    ASdb <- Splicingfinder(transdb,Ncor=1)
    ASdb <- ExonsCluster(ASdb,transdb)
    bamfiles <- rbind(samplebamfiles[,"path"])
    Total.splicingInfo <- ASdb@SplicingModel$"ES"
    each.ES.re <- rbind(ES.fi.result[ES.fi.result[,"Index"] == "ES3",])
    each.ranges <- rbind(unique(cbind(do.call(rbind,strsplit(each.ES.re[,"DownEX"],"-"))[,1],
        do.call(rbind,strsplit(each.ES.re[,"UpEX"],"-"))[,2])))
    group.1.spl <- c(split.splice(each.ES.re[,"Do_des"],each.ES.re[,"1st_des"]),
        split.splice(each.ES.re[,"1st_des"],each.ES.re[,"Up_des"]))
    group.2.spl <- split.splice(each.ES.re[,"Do_des"],each.ES.re[,"Up_des"])
    total.reads <- SplicingReads(bamfiles[1],each.ES.re[,c("DownEX","1stEX","UpEX")],
        c(group.1.spl,group.2.spl),each.ranges,each.ES.re[,"Nchr"],"paired")
    
## End(Not run)

IMAS documentation built on Nov. 8, 2020, 7:48 p.m.