plotSummarizedCov {RiboProfiling} | R Documentation

## Plots the summarized coverage in a specified range (e.g. around TSS) for the specified match sizes

### Description

Plots the summarized coverage in a specified range (e.g. around TSS) for the specified match sizes

### Usage

    plotSummarizedCov(covSummarized)

### Arguments

`covSummarized` | a list of GRanges objects. For each matchSize a GRanges object of the summarized coverage.

### Value

a ggplot2 plot of read coverage in interval

### Examples

    #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)

[Package RiboProfiling version 1.7.2 Index]