Read start coverage around the TSS on the predifined CDSs

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Description

Read start coverage around the TSS on the predifined CDSs

Usage

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readStartCov(alnGRanges, oneBinRanges, matchSize = "all", fixedInterval,
  renameChr, charPerc = "perc")

Arguments

alnGRanges

A GRanges object containing the alignment information. In order to improve the performance transform the GAlignments BAM object into a GRanges object containing cigar match size as metadata.

oneBinRanges

A GRanges object. Transform the gene GRangesList into one big GRanges object. Add the info on the cds_id.

matchSize

either "all" or a vector of read match sizes. If matchSize <- "all", then all the reads are used to compute the coverage. If the matchSize is a vector of read match sizes, the summarized coverage is reported per match size and for the sum up.

fixedInterval

a numeric vector with the extremities of the interval. Ex. fixedInterval <- c(-20,20) or fixedInterval <- c(0,40) ...

renameChr

a character object. It contains the name to be given to the new summarized coverage interval. Ex. renameChr <- "aroundTSS" the summarized region around the TSS.

charPerc

a character object. Either "perc" (the default) or "sum" for percentage of counts per position or the sum of counts per position.

Value

a list of GRanges objects (for each matchSize chosen). It contains the summarized coverage for the specified read match sizes.

Examples

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#read the BAM 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, percBestExpressed=0.01)

#the coverage in the TSS flanking region for the summarized read match sizes
listPromoterCov <- readStartCov(
     alnGRanges,
     oneBinRanges,
     matchSize="all",
     fixedInterval=c(-20, 20),
     renameChr="aroundTSS",
     charPerc="perc"
)