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

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

Check and, if possible, correct the chromosome names in a trans.ranges data.table

Description

Check and, if possible, correct the chromosome names in a trans.ranges data.table

Usage

CheckAndFixChrNamesForTransRanges(
  trans.ranges,
  vcf.df,
  ref.genome,
  name.of.VCF = NULL
)

Arguments

trans.ranges	A data.table which contains transcript range and strand information. Please refer to TranscriptRanges for more details.
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$CHROM values are correct or can be corrected, then a vector of chromosome names that can be used as a replacement for trans.ranges$chrom. If the names in vcf.df$CHROM cannot be made to be consistent with the chromosome names in trans.ranges$chrom, then stop.

ICAMS documentation built on June 15, 2025, 1:08 a.m.