ReadAndSplitStrelkaSBSVCFs function

Read and split Strelka SBS VCF files

Read and split Strelka SBS VCF files

The function will find and merge adjacent SBS pairs into DBS if their VAFs are very similar. The default threshold value for VAF is 0.02.

ReadAndSplitStrelkaSBSVCFs( files, names.of.VCFs = NULL, suppress.discarded.variants.warnings = TRUE )

Arguments

  • files: Character vector of file paths to the Strelka SBS VCF files.
  • names.of.VCFs: Optional. Character vector of names of the VCF files. The order of names in names.of.VCFs should match the order of VCF file paths in files. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) in files and file paths without extensions (and the leading dot) will be used as the names of the VCF files.
  • suppress.discarded.variants.warnings: Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.

Value

A list of elements as follows:

  • SBS.vcfs: List of data.frames of pure SBS mutations -- no DBS or 3+BS mutations.
  • DBS.vcfs: List of data.frames of pure DBS mutations -- no SBS or 3+BS mutations.
  • discarded.variants: Non-NULL only if there are variants that were excluded from the analysis. See the added extra column discarded.reason for more details.

Examples

file <- c(system.file("extdata/Strelka-SBS-vcf", "Strelka.SBS.GRCh37.s1.vcf", package = "ICAMS")) list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs(file)

See Also

StrelkaSBSVCFFilesToCatalog

  • Maintainer: Steve Rozen
  • License: GPL-3 | file LICENSE
  • Last published: 2024-02-09