aroundPromoter {RiboProfiling} | R Documentation

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

### 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)

[Package RiboProfiling version 1.7.2 Index]