rbamtools (version 2.16.17)

readPooledBamGapDf: 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

Examples

# NOT RUN {
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")
# }