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\name{getGenomeFaFile}
\Rdversion{1.1}
%\alias{extractTranscriptSeqs}
%\alias{extractTranscriptSeqs,ANY-method}
%\alias{extractTranscriptSeqs,ANY,ANY}
%\alias{extractTranscriptSeqs,ANY,EnsDb-method}
\alias{getGenomeFaFile}
\alias{getGenomeFaFile,EnsDb-method}
\title{Functionality related to DNA/RNA sequences}
\description{
Utility functions related to RNA/DNA sequences, such as extracting
RNA/DNA sequences for features defined in \code{Ensb}.
}
\usage{
\S4method{getGenomeFaFile}{EnsDb}(x, pattern="dna.toplevel.fa")
%\S4method{extractTranscriptSeqs}{ANY,EnsDb}(x, transcripts, filter)
}
\arguments{
(In alphabetic order)
%% \item{filter}{
%% A filter object extending \code{\linkS4class{BasicFilter}} or a list
%% of such object(s) to select specific entries from the database (see
%% examples below).
%% }
\item{pattern}{
For method \code{getGenomeFaFile}: the pattern to be used to
identify the fasta file representing genomic DNA sequence.
}
%% \item{transcripts}{
%% For \code{extractTranscriptSeqs}: the \code{EnsDb} object from which
%% the transcript definitions should be extracted.
%% }
\item{x}{
%% For \code{extractTranscriptSeqs}: An object representing a single
%% chromosome or a collection of chromosomes. Refer to the help of the
%% \code{\link[GenomicFeatures]{extractTranscriptSeqs}} method in
%% \code{GenomicFeatures} package for more information.
For all other methods an \code{EnsDb} instance.
}
}
\section{Methods and Functions}{
\describe{
%% \item{extractTranscriptSeqs}{
%% Extract transcript sequences. This method adapts the
%% \code{\link[GenomicFeatures]{extractTranscriptSeqs}} from the
%% \code{GenomicFeatures} package to allow the usage of filters to
%% specify the transcripts from which the sequence should be
%% extracted.
%% }
\item{getGenomeFaFile}{
Returns a \code{\link[Rsamtools]{FaFile-class}} (defined in
\code{Rsamtools}) with the genomic sequence of the genome build
matching the Ensembl version of the \code{EnsDb} object.
The file is retrieved using the \code{AnnotationHub} package,
thus, at least for the first invocation, an internet connection is
required to locate and download the file; subsequent calls will
load the cached file instead.
If no fasta file for the actual Ensembl version is available the
function tries to identify a file matchint the species and genome
build version of the closest Ensembl release and returns that
instead.
See the vignette for an example to work with such files.
}
}
}
\value{
For \code{getGenomeFaFile}: a \code{\link[Rsamtools]{FaFile-class}}
object with the genomic DNA sequence.
%% For \code{extractTranscriptSeqs}: A \code{DNAStringSet} object
%% parallel to \code{transcripts} (i.e. the i-th element in it is the
%% sequence of the i-th transcript in \code{transcripts}).
}
\author{
Johannes Rainer
}
\seealso{
\code{\link{transcripts}}
\code{\link{exonsBy}}
}
\examples{
## Loading an EnsDb for Ensembl version 86 (genome GRCh38):
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
\dontrun{
## Retrieve a FaFile with the gneomic DNA sequence matching the organism,
## genome release version and, if possible, the Ensembl version of the
## EnsDb object.
Dna <- getGenomeFaFile(edb)
## Extract the transcript sequence for all transcripts encoded on chromosome
## Y.
##extractTranscriptSeqs(Dna, edb, filter=SeqNameFilter("Y"))
}
}
\keyword{classes}
|
