startRegionString {ORFik}R Documentation

Get start region as DNA-strings per GRanges group

Description

One window per start site, if upstream and downstream are both 0, then only the startsite is returned.

Usage

startRegionString(grl, tx, faFile, upstream = 20, downstream = 20)

Arguments

grl

a GRangesList of ranges to find regions in.

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

Value

a character vector of start regions


[Package ORFik version 1.4.0 Index]