GenomicFeatures (version 1.24.2)

TxDb-class: TxDb objects

Description

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.

See Also

• makeTxDbFromUCSC,makeTxDbFromBiomart,makeTxDbFromGRanges, andmakeTxDbFromGFF, for convenient ways to make aTxDbobject from UCSC or BioMart online resources, or from aGRangesobject, or from a GFF or GTF file.
• saveDbandloadDbin theAnnotationDbipackage for saving and loading a TxDb object as an SQLite file.
• transcripts,transcriptsBy, andtranscriptsByOverlaps, for how to extract genomic features from a TxDb object.
• transcriptLengthsfor extracting the transcript lengths from aTxDbobject.
• select-methodsfor how to use the simple "select" interface to extract information from a TxDb object.
• TheFeatureDbclass for storing genomic locations of an arbitrary type of genomic features.
• TheSeqinfoclass in theGenomeInfoDbpackage.

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))