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\name{extendExonsIntoIntrons}
\alias{extendExonsIntoIntrons}
\title{
Extend exons by a given number of bases into their adjacent introns
}
\description{
\code{extendExonsIntoIntrons} extends the supplied exons by a given
number of bases into their adjacent introns.
}
\usage{
extendExonsIntoIntrons(ex_by_tx, extent=2)
}
\arguments{
\item{ex_by_tx}{
A \link[GenomicRanges]{GRangesList} object containing exons grouped
by transcript. This must be an object as returned by
\code{\link{exonsBy}(txdb, by="tx")}, that is:
\itemize{
\item each list element in \code{ex_by_tx} must be a
\link[GenomicRanges]{GRanges} object representing the
exons of a given transcript;
\item the exons in each list element must be ordered by ascending
rank with respect to their transcript.
}
}
\item{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 \emph{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 \link[GenomicRanges]{GRangesList} object \code{ex_by_tx}
where the original exon ranges have been extended.
Names and metadata columns on \code{ex_by_tx} are propagated to the
result.
}
\author{Hervé Pagès}
\seealso{
\itemize{
\item \code{\link{transcripts}}, \code{\link{transcriptsBy}},
and \code{\link{transcriptsByOverlaps}}, for extracting
genomic feature locations from a \link{TxDb}-like object.
\item \code{\link{exonicParts}} and \code{\link{intronicParts}} for
extracting non-overlapping exonic or intronic parts from a
TxDb-like object.
\item \code{\link{extractTranscriptSeqs}} for extracting transcript
(or CDS) sequences from chromosome sequences.
\item The \link{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))
}
\keyword{manip}
|
