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` | `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

[Package ORFik version 1.8.6 Index]