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\name{getGenomeFaFile}
\Rdversion{1.1}
\alias{getGenomeFaFile}
\alias{getGenomeFaFile,EnsDb-method}
\alias{getGenomeTwoBitFile}
\alias{getGenomeTwoBitFile,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{getGenomeTwoBitFile}{EnsDb}(x)
}
\arguments{
(In alphabetic order)
\item{pattern}{
For method \code{getGenomeFaFile}: the pattern to be used to
identify the fasta file representing genomic DNA sequence.
}
\item{x}{
An \code{EnsDb} instance.
}
}
\section{Methods and Functions}{
\describe{
\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 matching 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.
}
\item{getGenomeTwoBitFile}{
Returns a \code{\link{TwoBitFile-class}} (defined in the
\code{rtracklayer} package) with the genomeic sequence of the
genome build matching the Ensembl version of the \code{EnsDb}
object. The file is retrieved from \code{AnnotationHub} and hence
requires (at least for the first query) an active internet
connection to download the respective resource. If no DNA sequence
matching the Ensembl version of \code{x} is available, the
function tries to find the genomic sequence of the best matching
genome build (closest Ensembl release) and returns that.
See the \code{ensembldb} vignette for details.
}
}
}
\value{
For \code{getGenomeFaFile}: a \code{\link[Rsamtools]{FaFile-class}}
object with the genomic DNA sequence.
For \code{getGenomeTwoBitFile}: a \code{\link{TwoBitFile-class}}
object with the genome sequence.
}
\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 TwoBitFile with the gneomic DNA sequence matching the organism,
## genome release version and, if possible, the Ensembl version of the
## EnsDb object.
Dna <- getGenomeTwoBitFile(edb)
## Extract the transcript sequence for all transcripts encoded on chromosome
## Y.
##extractTranscriptSeqs(Dna, edb, filter=SeqNameFilter("Y"))
}
}
\keyword{classes}
|
