regions {GenomicFeatures} | R Documentation |
Functions that compute genomic regions of interest such as promotor,
upstream regions etc, from the genomic locations provided in data like
geneMouse
.
transcripts(genes, proximal = 500, distal = 10000) exons(genes) introns(genes)
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. |
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.
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.
M. Lawrence.
data(geneHuman) ## promoter 300bp up and down from TSS (threeprime from TES) transcripts(geneHuman, proximal = 300)