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

Description Usage Arguments Value

View source: R/feature_helpers.R

Description

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

Usage

1
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 from.

downstream

an integer, default (0), relative region to get downstream from

Value

a character vector of start regions


ORFik documentation built on March 27, 2021, 6 p.m.