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

In ORFik: Open Reading Frames in Genomics

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()

ORFik documentation built on March 27, 2021, 6 p.m.