matchSeqStyle: A wrapper for seqlevelsStyle

In JokingHero/ORFik: Open Reading Frames in Genomics

A wrapper for seqlevelsStyle

Description

To make sure chromosome naming is correct (chr1 vs 1 vs I etc)

Usage

matchSeqStyle(range, chrStyle = NULL)

Arguments

range	a ranged object, (GRanges, GAlignment etc)
chrStyle	a GRanges object, TxDb, FaFile, , a seqlevelsStyle or Seqinfo. (Default: NULL) to get seqlevelsStyle from. In addition if it is a Seqinfo object, seqinfo will be updated. Example of seqlevelsStyle update: Is chromosome 1 called chr1 or 1, is mitocondrial chromosome called MT or chrM etc. Will use 1st seqlevel-style if more are present. Like: c("NCBI", "UCSC") -> pick "NCBI"

Value

a GAlignment/GRanges object depending on input.

JokingHero/ORFik documentation built on Oct. 21, 2024, 11:42 a.m.