ICAMS (version 2.1.2)

ReadAndSplitStrelkaSBSVCFs: Read and split Strelka SBS VCF files.

Description

Read and split Strelka SBS VCF files.

Usage

ReadAndSplitStrelkaSBSVCFs(files, names.of.VCFs = NULL)

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.

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 which contain rows in the input that did not represent SBSs or DBSs.

4. multiple.alt Rows with multiple alternate alleles (removed from SBS.vcfs etc.)

See Also

StrelkaSBSVCFFilesToCatalog

Examples

# NOT RUN {
file <- c(system.file("extdata/Strelka-SBS-vcf",
                      "Strelka.SBS.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs(file)
# }