assignFirstExonsStartSite: Reassign the start positions of the first exons per group in...

In JokingHero/ORFik: Open Reading Frames in Genomics

Reassign the start positions of the first exons per group in grl

Description

Per group in GRangesList, assign the most upstream site.

Usage

assignFirstExonsStartSite(
  grl,
  newStarts,
  is.circular = all(isCircular(grl) %in% TRUE)
)

Arguments

grl	a GRangesList object
newStarts	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 start of "-" strand objects should be the max end in group, use ORFik:::sortPerGroup(grl) to get sorted grl.

Value

the same GRangesList with new start sites

See Also

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

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