plotSummarizedCov: Plots the summarized coverage in a specified range (e.g....

In RiboProfiling: Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

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)

RiboProfiling documentation built on Nov. 8, 2020, 5:26 p.m.