importVCFfiles {mutSignatures}

Import Mutation data from VCF files.

Description

Import Mutation data from VCF files. The columns are expected in the following order: c("CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT"). Optional columns can be present to inform about sample ID or other info.

Usage

importVCFfiles(vcfFiles, sampleNames = NULL)

Arguments

vcfFiles

character vector, includes the names of the VCF files to be analyzed

sampleNames

character vector with alternative sample names (otherwise, VCF file names will be ised to identify each sample).

Details

This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.

Value

a concatenated data.frame with all variants found in the input VCF files. Sample ID is stored in the "SAMPLEID" column.

Author(s)

Damiano Fantini, [e-mail]

References

More information and examples about mutational signature analysis can be found here:

1. GitHub Repo: https://github.com/dami82/mutSignatures/

2. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

3. Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/

4. Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6