readPooledBamGaps {rbamtools}R Documentation

readPooledBamGaps: Position data for alignments gaps from multiple BAM files.

Description

The function takes vectors of BAM-file names (plus accompanying names of BAM-index-files) and return a bamGapList object. The bamGapList object can be merged with other bamGapList objects and data can be extracted with the 'as.data.frame' method.

Usage

readPooledBamGaps(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

Value

bamGapList

Author(s)

Wolfgang Kaisers

Examples

bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
rpb<-readPooledBamGaps(bam)
rpdf<-readPooledBamGapDf(bam)
hist(rpdf$gqs)
[Package rbamtools version 2.16.11.2 Index]