Using the "select" interface on TranscriptDb objects

Description

select, cols and keys can be used together to extract data from a TranscriptDb object.

Details

In the code snippets below, x is a TranscriptDb object.

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

keys(x, keytype): Return 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): Show which kinds of data can be returned for the TranscriptDb object.

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

Author(s)

Marc Carlson

See Also

• transcripts, transcriptsBy, and transcriptsByOverlaps, for other ways to extract genomic features from a TranscriptDb object.

• The TranscriptDb class.

Examples

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

## 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)