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 a UCSC-style data frame.

WARNING: All the functions described in this man page are now defunct!

Please use transcripts, exons or intronsByTranscript on a TranscriptDb object instead.

Usage

transcripts_deprecated(genes, proximal = 500, distal = 10000)
exons_deprecated(genes)
introns_deprecated(genes)

Arguments

genes

A UCSC-style data frame i.e. a data frame with 1 row per transcript and at least the following columns: "name", "chrom", "strand", "txStart", "txEnd", "exonCount", "exonStarts", "exonEnds", "intronStarts" and "intronEnds". A value in any of the last 4 columns must be a comma-separated list of integers. Note that unlike what UCSC does the start values here must be 1-based, not 0-based.

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_deprecated, each element corresponds to a transcript, and there are columns for each type of region (promoter, threeprime, upstream, and downstream). For exons_deprecated, each element corresponds to an exon. For introns_deprecated, each element corresponds to an intron.

Author(s)

M. Lawrence.

See Also

transcripts, exons, intronsByTranscript, TranscriptDb-class


[Package GenomicFeatures version 1.14.2 Index]