Import and process individual BAM/SAM/BED alignment files using
getAlignGal and combine them into a single GAlignments.
A list of paths to the alignment files.
Arguments passed to
If there is only one BAM file, then simply return the output from
getAlignGal; otherwise, all processed alignments are pooled to form a single GAlignments object.
GAlignments object containning the (combined) processed alignments with the
User are recommanded to pool technical replicates but keep biological replicate separate for confirmation.
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# Retrieve system files extdata.dir <- system.file("extdata", package="RIPSeeker") bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE) bamFiles <- grep("PRC2", bamFiles, value=TRUE) # combine the alignments for technical replicates alignGal <- combineAlignGals(bamFiles=grep(pattern="SRR039214", bamFiles, value=TRUE, invert=TRUE), reverseComplement=TRUE, genomeBuild="mm9")
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