upstreamOfPerGroup: Get rest of objects upstream (exclusive)

In ORFik: Open Reading Frames in Genomics

Description

Per group get the part upstream of position upstreamOfPerGroup(tx, startSites(cds, asGR = TRUE)) will return the 5' utrs per transcript, usually used for interesting parts of the transcripts.

Usage

upstreamOfPerGroup(
  tx,
  upstreamOf,
  allowOutside = TRUE,
  is.circular = all(isCircular(tx) %in% TRUE)
)

Arguments

tx	a GRangesList, usually of Transcripts to be changed
upstreamOf	a vector of integers, for each group in tx, where is the the base after the new stop point of last valid exon.
allowOutside	a logical (T), can upstreamOf extend outside range of tx, can set boundary as a false hit, so beware.
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.

Value

a GRangesList of upstream part

See Also

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

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