downstreamFromPerGroup: Get rest of objects downstream (inclusive)

View source: R/gr_positions.R

downstreamFromPerGroupR Documentation

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()


Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.