select-methods {GenomicFeatures} | R Documentation |
select
, cols
and keys
can be used together to
extract data from a TranscriptDb object.
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.
Marc Carlson
transcripts
, transcriptsBy
,
and transcriptsByOverlaps
, for other ways to
extract genomic features from a TranscriptDb object.
The TranscriptDb class.
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)