R: readPooledBamGaps: Position data for alignments gaps from...

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 2.16.17 Index]