SplicingReads: Count a junction and paired-end reads

Description Usage Arguments Value Author(s) Examples

View source: R/SplicingReads.R

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

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    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

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    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.