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\name{disjointExons}
\alias{disjointExons}
\alias{disjointExons,TxDb-method}
\title{
Extract non-overlapping exon parts from an object
}
\description{
\code{disjointExons} extracts the non-overlapping exon parts from a
\link{TxDb} object or any other supported object.
WARNING: \code{disjointExons} is defunct in BioC 3.15. Please use
\code{\link{exonicParts}} instead.
}
\usage{
disjointExons(x, ...)
\S4method{disjointExons}{TxDb}(x, aggregateGenes=FALSE,
includeTranscripts=TRUE, ...)
}
\arguments{
\item{x}{
A \link{TxDb} object or any other supported object.
}
\item{...}{
Arguments to be passed to methods.
}
\item{aggregateGenes}{
For \code{disjointExons} : A \code{logical}. When \code{FALSE}
(default) exon fragments that overlap multiple genes are dropped.
When \code{TRUE}, all fragments are kept and the \code{gene_id}
metadata column includes all gene ids that overlap the exon fragment.
}
\item{includeTranscripts}{
For \code{disjointExons} : A \code{logical}. When \code{TRUE}
(default) a \code{tx_name} metadata column is included that
lists all transcript names that overlap the exon fragment.
}
}
\details{
\code{disjointExons} creates a \link[GenomicRanges]{GRanges} of
non-overlapping exon parts with metadata columns of gene_id and exonic_part.
Exon parts that overlap more than 1 gene can be dropped with
\code{aggregateGenes=FALSE}. When \code{includeTranscripts=TRUE}
a \code{tx_name} metadata column is included that lists all
transcript names that overlap the exon fragment. This function
replaces \code{prepareAnnotationForDEXSeq} in the \pkg{DEXSeq}
package.
}
\value{
A \link[GenomicRanges]{GRanges} object.
}
\author{
\code{disjointExons} was originally implemented by Mike Love and Alejandro
Reyes and then moved (and adapted) to \pkg{GenomicFeatures} by Valerie
Obenchain.
}
\seealso{
\code{\link{exonicParts}} for an improved version of \code{disjointExons}.
}
\keyword{methods}
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