select-methods: Using the "select" interface on TxDb objects

In GenomicFeatures: Conveniently import and query gene models

Description

select, columns and keys can be used together to extract data from a TxDb object.

Details

In the code snippets below, x is a TxDb 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, pattern, column, fuzzy): Return keys for the database contained in the TxDb object .

The keytype argument specifies the kind of keys that will be returned. By default keys will return the "GENEID" keys for the database.

If keys is used with pattern, it will pattern match on the keytype.

But if the column argument is also provided along with the pattern argument, then pattern will be matched against the values in column instead.

And if keys is called with column and no pattern argument, then it will return all keys that have corresponding values in the column argument.

Thus, the behavior of keys all depends on how many arguments are specified.

Use of the fuzzy argument will toggle fuzzy matching to TRUE or FALSE. If pattern is not used, fuzzy is ignored.

columns(x): Show which kinds of data can be returned for the TxDb object.

select(x, keys, columns, 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 columns and keytype arguments.

Author(s)

Marc Carlson

See Also

• AnnotationDb-class for more descriptsion of methods select,keytypes,keys and columns.

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

• The TxDb 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
columns(txdb)

## call select
res <- select(txdb, head(keys(txdb, "GENEID")),
              columns=c("GENEID","TXNAME"),
              keytype="GENEID")
head(res)

GenomicFeatures documentation built on April 2, 2021, 6 p.m.