downstreamFromPerGroup: Get rest of objects downstream (inclusive)

In JokingHero/ORFik: Open Reading Frames in Genomics

Get rest of objects downstream (inclusive)

Description

Per group get the part downstream of position. downstreamFromPerGroup(tx, startSites(threeUTRs, asGR = TRUE)) will return the 3' utrs per transcript as GRangesList, usually used for interesting parts of the transcripts.

Usage

downstreamFromPerGroup(
  tx,
  downstreamFrom,
  is.circular = all(isCircular(tx) %in% TRUE)
)

Arguments

tx	a GRangesList, usually of Transcripts to be changed
downstreamFrom	a vector of integers, for each group in tx, where is the new start point of first valid exon.
is.circular	logical, default FALSE if not any is: all(isCircular(grl) Where grl is the ranges checked. If TRUE, allow ranges to extend below position 1 on chromosome. Since circular genomes can have negative coordinates.

Details

If you don't want to include the points given in the region, use downstreamOfPerGroup

Value

a GRangesList of downstream part

See Also

Other GRanges: assignFirstExonsStartSite(), assignLastExonsStopSite(), downstreamOfPerGroup(), upstreamFromPerGroup(), upstreamOfPerGroup()

JokingHero/ORFik documentation built on Oct. 21, 2024, 11:42 a.m.