Check whether chromosome has at least one alignment to prevent abnormal behaviour of the subsequent functions. In case no alignment is found on an entire chromosome, add a pseudo-alignment as a placeholder for that chromosome.
GRanges object containing the alignment information.
In case no alignment is found on an entire chromosome, add an alignment with start 1 and end 20 as a placeholder for the chromosome. This step is necessary to maintian the chromosome information.
Original or augmented input GRanges object with pseudoreads, depending on whether there exists empty chromosome(s).
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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) alignGal <- getAlignGal(bamFiles, reverseComplement=TRUE, genomeBuild="mm9") alignGR <- as(alignGal, "GRanges") alignGR x <- addPseudoAlignment(alignGR) x
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