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\name{getTranscriptSeqs}
\alias{getTranscriptSeqs}
\alias{getTranscriptSeqs,GRangesList,ANY-method}
\alias{getTranscriptSeqs,GRangesList,BSgenome-method}
\alias{getTranscriptSeqs,GRangesList,FaFile-method}
\alias{getTranscriptSeqs,GRanges,FaFile-method}
\title{Get transcript sequences}
\description{
This function is defunct. Use GenomicFeatures::extractTranscriptSeqs()
instead.
Extract transcript sequences from a \link[BSgenome]{BSgenome} object or
an \link[Rsamtools]{FaFile}.
}
\usage{
\S4method{getTranscriptSeqs}{GRangesList,BSgenome}(query, subject, ...)
\S4method{getTranscriptSeqs}{GRangesList,FaFile}(query, subject, ...)
\S4method{getTranscriptSeqs}{GRanges,FaFile}(query, subject, ...)
}
\arguments{
\item{query}{A \link[GenomicRanges]{GRangesList} object containing
exons or cds grouped by transcript.
}
\item{subject}{A \link[BSgenome]{BSgenome} object or a \link[Rsamtools]{FaFile} from which
the sequences will be taken.
}
\item{\dots}{Additional arguments
}
}
\details{
\code{getTranscriptSeqs} is a wrapper for the
\code{extractTranscriptSeqs} and \code{getSeq} functions. The
purpose is to allow sequence extraction from either a
\link[BSgenome]{BSgenome} or \link[Rsamtools]{FaFile}. Transcript
sequences are extracted based on the boundaries of the feature
provided in the \code{query} (i.e., either exons or cds regions).
}
\value{
A \link[Biostrings]{DNAStringSet} instance containing the sequences for all transcripts
specified in \code{query}.
}
\author{Valerie Obenchain}
\seealso{
\link{predictCoding}
\link[GenomicFeatures]{extractTranscriptSeqs}
\link[Biostrings]{getSeq}
}
\examples{
## See ?extractTranscriptSeqs in the GenomicFeatures package.
}
\keyword{methods}
\keyword{manip}
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