orfRelativePos: Relative position of the start and stop codon along the...

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

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)

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