upstreamOfPerGroup {ORFik} | R Documentation |
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.
upstreamOfPerGroup( tx, upstreamOf, allowOutside = TRUE, is.circular = all(isCircular(tx) %in% TRUE) )
tx |
a |
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. |
a GRangesList of upstream part
Other GRanges:
assignFirstExonsStartSite()
,
assignLastExonsStopSite()
,
downstreamFromPerGroup()
,
downstreamOfPerGroup()
,
upstreamFromPerGroup()