readStartCov {RiboProfiling} | R Documentation

## Read start coverage around the TSS on the predifined CDSs

### Description

Read start coverage around the TSS on the predifined CDSs

### Usage

    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

    #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"
    )

[Package RiboProfiling version 1.16.0 Index]