regions {GenomicFeatures}R Documentation

Functions that compute genomic regions of interest.

Description

Functions that compute genomic regions of interest such as promotor, upstream regions etc, from the genomic locations provided in data like geneMouse.

Usage

transcripts(genes, proximal = 500, distal = 10000)
exons(genes)
introns(genes)

Arguments

genes A data.frame like that provided by geneMouse.
proximal The number of bases on either side of TSS and 3'-end for the promoter and end region, respectively.
distal The number of bases on either side for upstream/downstream, i.e. enhancer/silencer regions.

Details

The assumption made for introns is that there must be more than one exon, and that the introns are between the end of one exon and before the start of the next exon.

Value

All of these functions return a RangedData object with a gene column with the UCSC ID of the gene. For transcripts, each element corresponds to a transcript, and there are columns for each type of region (promoter, threeprime, upstream, and downstream). For exons, each element corresponds to an exon. For introns, each element corresponds to an intron.

Author(s)

M. Lawrence.

Examples

data(geneHuman)
## promoter 300bp up and down from TSS (threeprime from TES)
transcripts(geneHuman, proximal = 300)

[Package GenomicFeatures version 0.0.9 Index]