select-methods {GenomicFeatures} | R Documentation

## Using the "select" interface on TxDb objects

### 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)

[Package GenomicFeatures version 1.40.1 Index]