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\name{TxDb-class}
\alias{TxDb-class}
\alias{class:TxDb}
\alias{TxDb}
\alias{organism,TxDb-method}
\alias{seqlevels0,TxDb-method}
\alias{seqlevels<-,TxDb-method}
\alias{seqinfo,TxDb-method}
\alias{isActiveSeq}
\alias{isActiveSeq<-}
\alias{isActiveSeq,TxDb-method}
\alias{isActiveSeq<-,TxDb-method}
\alias{show,TxDb-method}
% coercion
\alias{as.list,TxDb-method}
\title{TxDb objects}
\description{
The TxDb class is a container for storing transcript annotations.
}
\section{Methods}{
In the code snippets below, \code{x} is a TxDb object.
\describe{
\item{}{
\code{metadata(x)}:
Return \code{x}'s metadata in a data frame.
}
\item{}{
\code{seqlevels0(x)}:
Get the \emph{sequence levels} originally in \code{x}. This ignores any
change the user might have made to the \emph{sequence levels} with the
\code{seqlevels} setter.
}
\item{}{
\code{seqlevels(x)}, \code{seqlevels(x) <- value}:
Get or set the \emph{sequence levels} in \code{x}.
}
\item{}{
\code{seqinfo(x)}, \code{seqinfo(x) <- value}:
Get or set the information about the underlying sequences.
Note that, for now, the setter only supports replacement of the
sequence names, i.e., except for their sequence names (accessed with
\code{seqnames(value)} and \code{seqnames(seqinfo(x))}, respectively),
\link[GenomeInfoDb]{Seqinfo} objects \code{value} (supplied) and
\code{seqinfo(x)} (current) must be identical.
}
\item{}{
\code{isActiveSeq(x)}:
Return the currently active sequences for this txdb object as a
named logical vector. Only active sequences will be tapped when
using the supplied accessor methods. Inactive sequences will be
ignored. By default, all available sequences will be active.
}
\item{}{
\code{isActiveSeq(x) <- value}:
Allows the user to change which sequences will be actively
accessed by the accessor methods by altering the contents of this
named logical vector.
}
\item{}{
\code{seqlevelsStyle(x)}, \code{seqlevelsStyle(x) <- value}:
Get or set the seqname style for \code{x}.
See the \link[GenomeInfoDb]{seqlevelsStyle} generic getter and setter
in the \pkg{GenomeInfoDb} package for more information.
}
\item{}{
\code{as.list(x)}:
Dump the entire db into a list of data frames, say \code{txdb_dump},
that can then be used to recreate the original db with
\code{do.call(makeTxDb, txdb_dump)} with no loss of information
(except possibly for some of the metadata).
Note that the transcripts are dumped in the same order in all the
data frames.
}
}
}
\author{Hervé Pagès, Marc Carlson}
\seealso{
\itemize{
\item \code{\link{makeTxDbFromUCSC}}, \code{\link{makeTxDbFromBiomart}},
and \code{\link{makeTxDbFromEnsembl}}, for making a \link{TxDb}
object from online resources.
\item \code{\link{makeTxDbFromGRanges}} and \code{\link{makeTxDbFromGFF}}
for making a \link{TxDb} object from a \link[GenomicRanges]{GRanges}
object, or from a GFF or GTF file.
\item \code{\link[AnnotationDbi]{saveDb}} and
\code{\link[AnnotationDbi]{loadDb}} in the \pkg{AnnotationDbi}
package for saving and loading a TxDb object as an SQLite file.
\item \code{\link{transcripts}}, \code{\link{transcriptsBy}},
and \code{\link{transcriptsByOverlaps}}, for extracting
genomic feature locations from a \link{TxDb}-like object.
\item \code{\link{transcriptLengths}} for extracting the transcript
lengths (and other metrics) from a \link{TxDb} object.
\item \link[GenomicFeatures]{select-methods} for how to use the
simple "select" interface to extract information from a
TxDb object.
\item The \link[GenomeInfoDb]{Seqinfo} class in the \pkg{GenomeInfoDb}
package.
}
}
\examples{
txdb_file <- system.file("extdata", "Biomart_Ensembl_sample.sqlite",
package="GenomicFeatures")
txdb <- loadDb(txdb_file)
txdb
## Use of seqinfo():
seqlevelsStyle(txdb)
seqinfo(txdb)
seqlevels(txdb)
seqlengths(txdb) # shortcut for 'seqlengths(seqinfo(txdb))'
isCircular(txdb) # shortcut for 'isCircular(seqinfo(txdb))'
names(which(isCircular(txdb)))
## You can set user-supplied seqlevels on 'txdb' to restrict any further
## operations to a subset of chromosomes:
seqlevels(txdb) <- c("Y", "6")
## Then you can restore the seqlevels stored in the db:
seqlevels(txdb) <- seqlevels0(txdb)
## Use of as.list():
txdb_dump <- as.list(txdb)
txdb_dump
txdb1 <- do.call(makeTxDb, txdb_dump)
stopifnot(identical(as.list(txdb1), txdb_dump))
}
\keyword{methods}
\keyword{classes}
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