Plots the summarized coverage in a specified range (e.g. around TSS) for the specified match sizes
a list of GRanges objects. For each matchSize a GRanges object of the summarized coverage.
a ggplot2 plot of read coverage in interval
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#read the BAM file into a GAlignments object using #GenomicAlignments::readGAlignments #the GAlignments object should be similar to ctrlGAlignments data(ctrlGAlignments) aln <- ctrlGAlignments #transform the GAlignments object into a GRanges object (faster processing) alnGRanges <- readsToStartOrEnd(aln, what="start") #make a txdb object containing the annotations for the specified species. #In this case hg19. txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene #Please make sure that seqnames of txdb correspond to #the seqnames of the alignment files ("chr" particle) #if not rename the txdb seqlevels #renameSeqlevels(txdb, sub("chr", "",seqlevels(txdb))) #get the flanking region around the promoter of the best expressed CDSs oneBinRanges <- aroundPromoter(txdb, alnGRanges) #the read start coverage around the TSS as a percentage for all match sizes. covSummarized <- readStartCov(alnGRanges, oneBinRanges, matchSize="all", c(-20,20), "aroundTSS", charPerc="perc") trackPlotTSS <- plotSummarizedCov(covSummarized) print(trackPlotTSS)
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