TranscriptDb-class {GenomicFeatures}R Documentation

TranscriptDb objects

Description

The TranscriptDb class is a container for storing transcript annotations. The FeatureDb class is a container for storing more generic GenomicFeature annotations.

See ?makeTranscriptDbFromUCSC and ?makeTranscriptDbFromBiomart for making a TranscriptDb object from the UCSC or BioMart sources.

See ?makeFeatureDbFromUCSC for making a FeatureDb object from the UCSC or BioMart sources.

See ?saveDb and ?loadDb for saving and loading the database contents of a TranscriptDb or FeatureDb object.

select, cols and keys are used together to extract data from an TranscriptDb object.

Methods

In the code snippets below, x is a TranscriptDb object. For the metadata and show methods, there is also support for FeatureDb objects.

metadata(x): Returns x's metadata in a data frame.

seqinfo(x): Gets the information about the underlying sequences as a Seqinfo object.

as.list(x): Dumps the entire db into a list of data frames txdump that can be used in do.call(makeTranscriptDb, txdump) to make the db again with no loss of information. Note that the transcripts are dumped in the same order in all the data frames.

isActiveSeq(x): Returns 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) <-: Allows the user to change which sequences will be actively accessed by the accessor methods by altering the contents of this named logical vector.

keytypes(x): allows the user to discover which keytypes can be passed in to select or keys and the keytype argument.

keys(x, keytype): returns keys for the database contained in the TranscriptDb object . By default it will return the "TXNAME" keys for the database, but if used with the keytype argument, it will return the keys from that keytype.

cols(x): shows which kinds of data can be returned for the TranscriptDb object.

select(x, keys, cols, keytype): When all the appropriate arguments are specifiedm select will retrieve the matching data as a data.frame based on parameters for selected keys and cols and keytype arguments.

See ?transcripts, ?transcriptsByOverlaps, ?id2name and ?transcriptsBy for other useful operations on TranscriptDb objects.

Author(s)

H. Pages, Marc Carlson

See Also

Seqinfo-class, makeTranscriptDbFromUCSC, makeTranscriptDbFromBiomart, loadFeatures, transcripts, transcriptsByOverlaps, id2name, transcriptsBy

Examples

txdb_file <- system.file("extdata", "Biomart_Ensembl_sample.sqlite",
                         package="GenomicFeatures")
txdb <- loadFeatures(txdb_file)
txdb

## Use of seqinfo
seqinfo(txdb)
seqlevels(txdb)  # shortcut for 'seqlevels(seqinfo(txdb))'
seqlengths(txdb)  # shortcut for 'seqlengths(seqinfo(txdb))'
isCircular(txdb)  # shortcut for 'isCircular(seqinfo(txdb))'
names(which(isCircular(txdb)))

## Examples on how to change which sequences are active
## Set chr1 and chr3 to be inactive:
isActiveSeq(txdb)[c("1", "3")] <- FALSE
## Set ALL of the chromsomed to be inactive
isActiveSeq(txdb)[seqlevels(txdb)] <- FALSE
## Now set only chr1 and chr5 to be active
isActiveSeq(txdb)[c("1", "4")] <- TRUE

## Use of as.list
txdump <- as.list(txdb)
txdump
txdb1 <- do.call(makeTranscriptDb, txdump)
stopifnot(identical(as.list(txdb1), txdump))

## Use of select and supporting methods
## find key types
keytypes(txdb)
## list IDs that can be used to filter
head(keys(txdb, "GENEID"))
head(keys(txdb, "TXID"))
head(keys(txdb, "TXNAME"))
## list columns that can be returned by select
cols(txdb)
## call select
res = select(txdb, head(keys(txdb, "GENEID")),
             cols = c("GENEID","TXNAME"),
             keytype="GENEID")
head(res)

[Package GenomicFeatures version 1.6.1 Index]