extractBamRegions: extractBamRegions: Extraction of alignments from given...
In rbamtools: Read and Write BAM (Binary Alignment) Files

Description Usage Arguments Details Value Author(s) Examples

The function extractBamRegions writes aligns or some part of the stored aligns in a BAM file as reads into a BAM output file.

1	extractBamRegions(bamFiles, ranges, idxFiles, outFiles)

bamFiles

character: Vector of BAM file names.

ranges

data.frame: Must contain three columns seqid, start and end. The seqid

idxFiles

character: Vector of BAM index file names.

outFiles

character: Vector of output file names.

bamFiles, idxFiles and outFiles are checked for equal length. bamFiles and idxFiles are checked for existance. There are sensible default values given for idxFiles and outFiles. The default location for writing output files is the current working directory.

No return value given

Wolfgang Kaisers

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bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
gene_pos <- data.frame(seqid="chr1", start=15e3, end=20e3)
extractBamRegions(bam, gene_pos)