transcripts {GenomicFeatures}R Documentation

Extract genomic features from an object

Description

Generic functions to extract genomic features from an object. This page documents the methods for TranscriptDb objects only.

Usage

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")

#promoters(x, upstream=2000, downstream=200, ...)
## S4 method for signature 'TranscriptDb'
promoters(x, upstream=2000, downstream=200, ...)

microRNAs(x)
## S4 method for signature 'TranscriptDb'
microRNAs(x)

tRNAs(x)
## S4 method for signature 'TranscriptDb'
tRNAs(x)

Arguments

x

A TranscriptDb object.

...

Arguments to be passed to or from methods.

vals

Either NULL or a named list of vectors to be used to restrict the output. Valid names for this list are: "gene_id", "tx_id", "tx_name", "tx_chrom", "tx_strand", "exon_id", "exon_name", "exon_chrom", "exon_strand", "cds_id", "cds_name", "cds_chrom", "cds_strand" and "exon_rank".

columns

Columns to include in the output. Must be NULL or a character vector with values in the above list of valid names. With the following restrictions:

  • "tx_chrom" and "tx_strand" are not allowed for transcripts.

  • "exon_chrom" and "exon_strand" are not allowed for exons.

  • "cds_chrom" and "cds_strand" are not allowed for cds.

If the vector is named, those names are used for the corresponding column in the element metadata of the returned object.

upstream

For promoters() : An integer(1) value indicating the number of bases upstream from the transcription start site. For additional details see ?'promoters,GRanges-method'.

downstream

For promoters() : An integer(1) value indicating the number of bases downstream from the transcription start site. For additional details see ?'promoters,GRanges-method'.

Details

These are the main functions for extracting transcript information from a TranscriptDb object. With the exception of microRNAs, these methods can restrict the output based on categorical information. To restrict the output based on interval information, use the transcriptsByOverlaps, exonsByOverlaps, and cdsByOverlaps functions.

The promoters() function computes user-defined promoter regions for the transcripts in a TranscriptDb object. The return object is a GRanges of promoter regions around the transcription start site the span of which is defined by upstream and downstream. For additional details on how the promoter range is computed and the handling of + and - strands see ?'promoters,GRanges-method'.

Value

a GRanges object

Author(s)

M. Carlson, P. Aboyoun and H. Pages

See Also

Examples

## transcripts() and exons() :
  txdb <- loadDb(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"))

## microRNAs() :
## Not run: library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(mirbase.db)
microRNAs(TxDb.Hsapiens.UCSC.hg19.knownGene)

## End(Not run)

## promoters() :
head(promoters(txdb, 100, 50))
[Package GenomicFeatures version 1.12.2 Index]