orfRelativePos {RiboProfiling} | R Documentation

## Relative position of the start and stop codon along the transcript

### Description

Relative position of the start and stop codon along the transcript

### Usage

    orfRelativePos(cdsTransc, exonGRanges)

### Arguments

`cdsTransc` | a GRangesList. It contains the CDS coordinates grouped by transcript.
`exonGRanges` | a GRangesList. It contains the exon coordinates grouped by transcript.

### Value

a list. A list of relative positions of the start and end of ORFs.

### Examples

    #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

    #get all CDSs by transcript
    cds <- GenomicFeatures::cdsBy(txdb, by="tx", use.names=TRUE)

    #get all exons by transcript
    exonGRanges <- GenomicFeatures::exonsBy(txdb, by="tx", use.names=TRUE)

    #retrieve the positions of start and end codons relative to the transcript
    cdsPosTransc <- orfRelativePos(cds, exonGRanges)

[Package RiboProfiling version 1.16.0 Index]