assignLastExonsStopSite: Reassign the stop positions of the last exons per group

In JokingHero/ORFik: Open Reading Frames in Genomics

Reassign the stop positions of the last exons per group

Description

Per group in GRangesList, assign the most downstream site.

Usage

assignLastExonsStopSite(
  grl,
  newStops,
  is.circular = all(isCircular(grl) %in% TRUE)
)

Arguments

grl	a GRangesList object
newStops	an integer vector of same length as grl, with new start values (absolute coordinates, not relative)
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

make sure your grl is sorted, since stop of "-" strand objects should be the min start in group, use ORFik:::sortPerGroup(grl) to get sorted grl.

Value

the same GRangesList with new stop sites

See Also

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

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.