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

readPooledBamGapDf {rbamtools} | R Documentation

## readPooledBamGapDf: 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 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

### Author(s)

Wolfgang Kaisers

### 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")

[Package rbamtools version 2.16.17 Index]