startRegionString: Get start region as DNA-strings per GRanges group

In JokingHero/ORFik: Open Reading Frames in Genomics

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	FaFile, BSgenome, fasta/index file path or an ORFik experiment. This file is usually used to find the transcript sequences from some GRangesList.
upstream	an integer, default (0), relative region to get upstream end from. (0 means start site, +1 is one upstream, -1 is one downstream)
downstream	an integer, default (0), relative region to get downstream end from (0 means start site, +1 is one downstream, -1 is one upstream)

Value

a character vector of start regions

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.