| TxDb-class {GenomicFeatures} | R Documentation |
The TxDb class is a container for storing transcript annotations.
See ?FeatureDb for a more generic container for storing
genomic locations of an arbitrary type of genomic features.
See ?makeTxDbFromUCSC and
?makeTxDbFromBiomart for convenient ways to
make TxDb objects from UCSC or BioMart online resources.
See ?makeTxDbFromGFF for making a TxDb
object from annotations available as a GFF3 or GTF file.
In the code snippets below, x is a TxDb object.
metadata(x):
Return x's metadata in a data frame.
seqinfo(x), 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
seqnames(value) and seqnames(seqinfo(x)), respectively),
Seqinfo objects value (supplied) and
seqinfo(x) (current) must be identical.
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.
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.
seqlevelsStyle(x), seqlevelsStyle(x) <- value:
Get or set the seqname style for x.
See the seqlevelsStyle generic getter and setter
in the GenomeInfoDb package for more information.
as.list(x):
Dump the entire db into a list of data frames, say txdb_dump,
that can then be used to recreate the original db with
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.
H. Pages, Marc Carlson
makeTxDbFromUCSC, makeTxDbFromBiomart,
makeTxDbFromGRanges, and makeTxDbFromGFF,
for convenient ways to make a TxDb object from UCSC or BioMart
online resources, or from a GRanges object,
or from a GFF or GTF file.
saveDb and loadDb for
saving and loading the database content of a TxDb object.
transcripts, transcriptsBy,
and transcriptsByOverlaps,
for how to extract genomic features from a TxDb object.
transcriptLengths for extracting the transcript
lengths from a TxDb object.
select-methods for how to use the simple "select" interface to extract information from a TxDb object.
The FeatureDb class for storing genomic locations of an arbitrary type of genomic features.
The Seqinfo class in the GenomeInfoDb package.
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)))
## Can set txdb so that only chr1 and chr2 are used by using the
## seqlevels:
seqlevels(txdb, force=TRUE) <- c("1", "2")
## Then you can restore the default seqlevels:
txdb <- restoreSeqlevels(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))