CheckAndFixChrNamesForTransRanges: Check and, if possible, correct the chromosome names in a...
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

View source: R/chromosome_name_functions.R

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

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

`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.

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 April 3, 2021, 5:07 p.m.