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

Description Usage Arguments Value Examples

Description

Relative position of the start and stop codon along the transcript

Usage

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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

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#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)


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