rangeBasedAccessors {OrganismDbi}R Documentation

Extract genomic features from an object

Description

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

Usage

## S4 method for signature 'OrganismDb'
transcripts(x, vals=NULL, columns=c("TXID", "TXNAME"))

## S4 method for signature 'OrganismDb'
exons(x, vals=NULL, columns="EXONID")

## S4 method for signature 'OrganismDb'
cds(x, vals=NULL, columns="CDSID")

## S4 method for signature 'OrganismDb'
transcriptsBy(x, by, columns)

## S4 method for signature 'OrganismDb'
exonsBy(x, by, columns)

## S4 method for signature 'OrganismDb'
cdsBy(x, by, columns)

Arguments

x

A TranscriptDb object.

...

Arguments to be passed to or from methods.

by

One of "gene", "exon", "cds" or "tx". Determines the grouping.

columns

The columns or kinds of metadata that can be retrieved from the database. All possible columns are returned by using the columns method.

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".

Details

These are the range based functions for extracting transcript information from a OrganismDb object.

Value

a GRanges or GRangesList object

Author(s)

M. Carlson

See Also

Examples

## extracting all transcripts from Homo.sapiens with some extra metadata
library(Homo.sapiens)
cols = c("TXNAME","SYMBOL")
res <- transcripts(Homo.sapiens, columns=cols)

## extracting all transcripts from Homo.sapiens, grouped by gene and
## with extra metadata
res <- transcriptsBy(Homo.sapiens, by="gene", columns=cols)

## list possible values for columns argument:
columns(Homo.sapiens)
[Package OrganismDbi version 1.4.0 Index]