TxDb-class {GenomicFeatures} | R Documentation

## 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.

### Methods

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.

### Author(s)

Hervé Pagès, Marc Carlson

### See Also

- `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.

### 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))

[Package GenomicFeatures version 1.39.7 Index]