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\name{seqlevelsStyle}
\Rdversion{1.1}
\alias{seqlevelsStyle}
\alias{seqlevelsStyle,EnsDb-method}
\alias{seqlevelsStyle<-}
\alias{seqlevelsStyle<-,EnsDb-method}
\alias{supportedSeqlevelsStyles}
\alias{supportedSeqlevelsStyles,EnsDb-method}
\title{Support for other than Ensembl seqlevel style}
\description{
The methods and functions on this help page allow to integrate
\code{EnsDb} objects and the annotations they provide with other
Bioconductor annotation packages that base on chromosome names
(seqlevels) that are different from those defined by Ensembl.
}
\usage{
\S4method{seqlevelsStyle}{EnsDb}(x)
\S4method{seqlevelsStyle}{EnsDb}(x) <- value
\S4method{supportedSeqlevelsStyles}{EnsDb}(x)
}
\arguments{
(In alphabetic order)
\item{value}{
For \code{seqlevelsStyle<-}: a character string specifying the
seqlevels style that should be set. Use the
\code{supportedSeqlevelsStyle} to list all available and supported
seqlevel styles.
}
\item{x}{
An \code{EnsDb} instance.
}
}
\section{Methods and Functions}{
\describe{
\item{seqlevelsStyle}{
Get the style of the seqlevels in which results returned from the
\code{EnsDb} object are encoded. By default, and internally,
seqnames as provided by Ensembl are used.
The method returns a character string specifying the currently used
seqlevelstyle.
}
\item{seqlevelsStyle<-}{
Change the style of the seqlevels in which results returned from
the \code{EnsDb} object are encoded. Changing the seqlevels helps
integrating annotations from \code{EnsDb} objects e.g. with
annotations from packages that base on UCSC annotations.
}
\item{supportedSeqlevelsStyles}{
Lists all seqlevel styles for which mappings between seqlevel
styles are available in the \code{GenomeInfoDb} package.
The method returns a character vector with supported seqlevel
styles for the organism of the \code{EnsDb} object.
}
}
}
\note{
The mapping between different seqname styles is performed based on
data provided by the \code{GenomeInfoDb} package. Note that in most
instances no mapping is provided for seqnames other than for primary
chromosomes. By default functions from the \code{ensembldb} package
return the \emph{original} seqname is in such cases. This behaviour
can be changed with the \code{ensembldb.seqnameNotFound} global
option. For the special keyword \code{"ORIGINAL"} (the default), the
original seqnames are returned, for \code{"MISSING"} an error is
thrown if a seqname can not be mapped. In all other cases, the value
of the option is returned as seqname if no mapping is available
(e.g. setting \code{options(ensembldb.seqnameNotFound=NA)} returns an
\code{NA} if the seqname is not mappable).
}
\value{
For \code{seqlevelsStyle}: see method description above.
For \code{supportedSeqlevelsStyles}: see method description above.
}
\author{
Johannes Rainer
}
\seealso{
\code{\linkS4class{EnsDb}}
\code{\link{transcripts}}
}
\examples{
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
## Get the internal, default seqlevel style.
seqlevelsStyle(edb)
## Get the seqlevels from the database.
seqlevels(edb)
## Get all supported mappings for the organism of the EnsDb.
supportedSeqlevelsStyles(edb)
## Change the seqlevels to UCSC style.
seqlevelsStyle(edb) <- "UCSC"
seqlevels(edb)
## Change the option ensembldb.seqnameNotFound to return NA in case
## the seqname can not be mapped form Ensembl to UCSC.
options(ensembldb.seqnameNotFound = NA)
seqlevels(edb)
## Restoring the original setting.
options(ensembldb.seqnameNotFound = "ORIGINAL")
}
\keyword{classes}
|
