TxDb objects
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.
In the code snippets below, x is a TxDb object.
metadata(x):
Return x's metadata in a data frame.
seqlevels0(x):
Get the sequence levels originally in x. This ignores any
change the user might have made to the sequence levels with the
seqlevels setter.
seqlevels(x), seqlevels(x) <- value:
Get or set the sequence levels in x.
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.
Hervé Pagès, Marc Carlson
makeTxDbFromUCSC, makeTxDbFromBiomart,
and makeTxDbFromEnsembl, for making a TxDb
object from online resources.
makeTxDbFromGRanges and makeTxDbFromGFF
for making a TxDb object from a GRanges
object, or from a GFF or GTF file.
saveDb and
loadDb in the AnnotationDbi
package for saving and loading a TxDb object as an SQLite file.
transcripts, transcriptsBy,
and transcriptsByOverlaps, for extracting
genomic feature locations from a TxDb-like object.
transcriptLengths for extracting the transcript
lengths (and other metrics) 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)))
## 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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.