ICAMS (version 2.0.7)

ReadAndSplitStrelkaSBSVCFs: Read and split Strelka SBS VCF files.

Description

Read and split Strelka SBS VCF files.

Usage

ReadAndSplitStrelkaSBSVCFs(files)

Arguments

files

Character vector of file paths to the Strelka SBS VCF files.

Value

A list of 3 in-memory objects as follows:

  1. SBS.vcfs List of data.frames of pure SBS mutations -- no DBS or 3+BS mutations.

  2. DBS.vcfs List of data.frames of pure DBS mutations -- no SBS or 3+BS mutations.

  3. ThreePlus List of data.tables with the key CHROM, LOW.POS, HIGH.POS. containing rows that that in the input that did not represent SBSs or DBSs.

See Also

StrelkaSBSVCFFilesToCatalog

Examples

Run this code
# NOT RUN {
file <- c(system.file("extdata",
                      "Strelka.SBS.GRCh37.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs(file)
# }

Run the code above in your browser using DataCamp Workspace