regions {GenomicFeatures} | R Documentation |
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.
transcripts_deprecated(genes, proximal = 500, distal = 10000) exons_deprecated(genes) introns_deprecated(genes)
genes |
A UCSC-style data frame i.e. a data frame with 1 row per transcript
and at least the following columns: |
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_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.
M. Lawrence.
transcripts
,
exons
,
intronsByTranscript
,
TranscriptDb-class