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

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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 15, 2025, 1:08 a.m.