extendExonsIntoIntrons: Extend exons by a given number of bases into their adjacent...

In Bioconductor/GenomicFeatures: Query the gene models of a given organism/assembly

Extend exons by a given number of bases into their adjacent introns

Description

extendExonsIntoIntrons extends the supplied exons by a given number of bases into their adjacent introns.

Usage

extendExonsIntoIntrons(ex_by_tx, extent=2)

Arguments

ex_by_tx

A GRangesList object containing exons grouped by transcript. This must be an object as returned by exonsBy(txdb, by="tx"), that is: each list element in ex_by_tx must be a GRanges object representing the exons of a given transcript; the exons in each list element must be ordered by ascending rank with respect to their transcript.

extent

Size of the extent in number of bases. 2 by default. The first exon in a transcript will be extended by that amount on its 3' side only. The last exon in a transcript will be extended by that amount on its 5' side only. All other exons (i.e. intermediate exons) will be extended by that amount on each side. Note that exons that belong to a single-exon transcript don't get extended. The default value of 2 corresponds to inclusion of the donor/acceptor intronic regions (typically GT/AG).

Value

A copy of GRangesList object ex_by_tx where the original exon ranges have been extended.

Names and metadata columns on ex_by_tx are propagated to the result.

Author(s)

Hervé Pagès

See Also

• transcripts, transcriptsBy, and transcriptsByOverlaps, for extracting genomic feature locations from a TxDb-like object.

• exonicParts and intronicParts for extracting non-overlapping exonic or intronic parts from a TxDb-like object.

• extractTranscriptSeqs for extracting transcript (or CDS) sequences from chromosome sequences.

• The TxDb class.

Examples

## With toy transcripts:
ex_by_tx <- GRangesList(
    TX1="chr1:10-20:+",
    TX2=c("chr1:10-20:+", "chr1:50-75:+"),
    TX3=c("chr1:10-20:+", "chr1:50-75:+", "chr1:100-120:+"),
    TX4="chr1:10-20:-",
    TX5=c("chr1:10-20:-", "chr1:50-75:-"),
    TX6=c("chr1:10-20:-", "chr1:50-75:-", "chr1:100-120:-")
)

extended <- extendExonsIntoIntrons(ex_by_tx, extent=2)
extended[1:3]
extended[4:6]

## With real-world transcripts:
library(TxDb.Celegans.UCSC.ce11.ensGene)
txdb <- TxDb.Celegans.UCSC.ce11.ensGene
ex_by_tx <- exonsBy(txdb, by="tx")
ex_by_tx

extendExonsIntoIntrons(ex_by_tx, extent=2)

## Sanity check:
stopifnot(identical(extendExonsIntoIntrons(ex_by_tx, extent=0), ex_by_tx))

Bioconductor/GenomicFeatures documentation built on Nov. 7, 2024, 4:25 a.m.