rbamtools (version 2.4.0)

readPooledBamGapDf: readPooledBamGapDf

Description

The function takes vectors of BAM-file names (plus accompanying names of BAM-index-files) and returns extracted data as data.frame. The data frame contains coordinates of align gaps plus a gap-quality-score (gqs) which quantifies information amount for detection of splice sites.

Usage

readPooledBamGapDf(infiles,idxInfiles=paste(infiles,".bai",sep=""))

Arguments

infiles

Filenames of BAM-files to be opened for data extraction.

idxInfiles

Optional: Name of BAM-index files

Examples

bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
rpb<-readPooledBamGaps(bam)
rpdf<-readPooledBamGapDf(bam)
hist(rpdf$gqs,las=1,xlab="",main="Gap quality score")