CheckAndFixChrNames: Check and, if possible, correct the chromosome names in a VCF...

View source: R/chromosome_name_functions.R

CheckAndFixChrNamesR Documentation

Check and, if possible, correct the chromosome names in a VCF data.frame.

Description

Check and, if possible, correct the chromosome names in a VCF data.frame.

Usage

CheckAndFixChrNames(vcf.df, ref.genome, name.of.VCF = NULL)

Arguments

vcf.df

A VCF as a data.frame. Check the names in column CHROM.

ref.genome

The reference genome with the chromosome names to check vcf.df$CHROM against; must be a Bioconductor BSgenome, e.g. BSgenome.Hsapiens.UCSC.hg38.

name.of.VCF

Name of the VCF file.

Value

If the vcf.df$CHROM values are correct or can be corrected, then a vector of chromosome names that can be used as a replacement for vcf.df$CHROM. If the names in vcf.df$CHROM cannot be made to be consistent with the chromosome names in ref.genome, then stop.


ICAMS documentation built on June 22, 2024, 6:47 p.m.