aroundPromoter: Returns the flank size around the TSS for the x % CDSs

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

Description

Returns the flank size around the TSS for the x % CDSs

Usage

aroundPromoter(txdb, alnGRanges, percBestExpressed, flankSize)

Arguments

txdb	a TxDb object containing the annotations info to intersect with the alignment files.
alnGRanges	A GRanges object containing the alignment information. In order to improve the performance of this function the GAlignments BAM object should be transformed into a GRanges object containing the cigar match size information as metadata.
percBestExpressed	a numeric [between 0 and 1]. The percentage of the best expressed CDSs on which to plot the coverage around the TSS. Necessary if the shiftValue parameter must be estimated. Default value 0.03 (3%).
flankSize	a numeric positive integer. How many bp left and right of the TSS should the coverage be performed? Ex. flankSize <- 20

Value

A GRanges object containing the 1 bp ranges for the selected CDSs in the TSS defined flanking region.

Examples

#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)

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