upstreamOfPerGroup: Get rest of objects upstream (exclusive)

Description Usage Arguments Value See Also

View source: R/gr_positions.R

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

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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.