startRegionString {ORFik} | R Documentation |
One window per start site, if upstream and downstream are both 0, then only the startsite is returned.
startRegionString(grl, tx, faFile, upstream = 20, downstream = 20)
grl |
a |
tx |
a GRangesList of transcripts or (container region), names of tx must contain all gr names. The names of gr can also be the ORFik orf names. that is "txName_id" |
faFile |
a FaFile from the fasta file, see ?FaFile. Can also be path to fastaFile with fai file in same dir. |
upstream |
an integer (0), relative region to get upstream from. |
downstream |
an integer (0), relative region to get downstream from |
a character vector of start regions