ICAMS (version 3.0.11)

ReadAndSplitStrelkaSBSVCFs: [Deprecated, use ReadAndSplitVCFs(variant.caller = "strelka") instead] Read and split Strelka SBS VCF files

Description

[Deprecated, use ReadAndSplitVCFs(variant.caller = "strelka") instead] 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.

Usage

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

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.

See Also

StrelkaSBSVCFFilesToCatalog

Examples

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