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

View source: R/gr_positions.R

assignFirstExonsStartSiteR Documentation

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()


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