transcripts {GenomicFeatures} | R Documentation |
Generic functions to extract genomic features from an object. This page documents the methods for TranscriptDb objects only.
transcripts(x, ...) ## S4 method for signature 'TranscriptDb' transcripts(x, vals=NULL, columns=c("tx_id", "tx_name")) exons(x, ...) ## S4 method for signature 'TranscriptDb' exons(x, vals=NULL, columns="exon_id") cds(x, ...) ## S4 method for signature 'TranscriptDb' cds(x, vals=NULL, columns="cds_id")
x |
A TranscriptDb object. |
... |
Arguments to be passed to or from methods. |
vals |
Either |
columns |
Columns to include in the output.
Must be
|
These are the main functions for extracting transcript information from
a TranscriptDb object. They can restrict the output based on
categorical information. To restrict the output based on interval
information, use the transcriptsByOverlaps
,
exonsByOverlaps
, and cdsByOverlaps
functions.
a GRanges object
M. Carlson, P. Aboyoun and H. Pages
TranscriptDb,
id2name
, transcriptsBy
,
transcriptsByOverlaps
txdb <- loadFeatures(system.file("extdata", "UCSC_knownGene_sample.sqlite", package="GenomicFeatures")) vals <- list(tx_chrom = c("chr3", "chr5"), tx_strand = "+") transcripts(txdb, vals) exons(txdb, vals=list(exon_id=1), columns=c("exon_id", "tx_name")) exons(txdb, vals=list(tx_name="uc009vip.1"), columns=c("exon_id", "tx_name"))