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

Description Usage Arguments Details Value Author(s) Examples

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

1	extractGeneRegions(src, trg, gl)

src

sampleBamFiles: List of source BAM files where alignments are read from. BAM index files must exist and be present in src object.

trg

sampleBamFiles: List of target BAM files where alignments are written to.

`gl`	`geneList`: Objects from which genetic regions are taken.

Reference sequence names in geneList object must all match sequence names in source BAM files.

Numeric. Number of written alignments for each file.

Wolfgang Kaisers

# + + + + + + + + + + + + + + + + + + #
# A) Create sampleBamFiles objects
# + + + + + + + + + + + + + + + + + + #
bam <- system.file("extdata","accepted_hits.bam",package="rbamtools")
outdir <- tempdir()
# Input sampleBamFiles object
ibs <- sampleBamFiles(bam)
# Output sampleBamFiles object
obs <- sampleBamFiles(file.path(outdir, "outu.bam"))
# + + + + + + + + + + + + + + + + + + #
# B) Create geneList Object
# + + + + + + + + + + + + + + + + + + #
rfile <- system.file("extdata",
            "hs.ucsc.small.RData",
                package="refGenome")

ucr <- loadGenome(rfile)
gt <- getGeneTable(ucr)
gl <- geneList(ucr, gt$gene_id)

extractGeneRegions(ibs, obs, gl)
bamFiles(obs) <- file.path(outdir, bamSort(obs, "out"))
bamIdxFiles(obs) <- paste(bamFiles(obs), "bai", sep=".")
createIndex(obs)