importVCFfiles

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

vcfFiles

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

sampleNames

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.

Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The framework includes modules that support raw data import and processing, mutational signature extraction, and results interpretation and visualization. The framework accepts widely used file formats storing information about DNA variants, such as Variant Call Format files. The framework performs Non-Negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. Bootstrapping is performed as part of the analysis. The framework supports parallelization and is optimized for use on multi-core systems. The software was described by Fantini D et al (2020) <doi:10.1038/s41598-020-75062-0> and is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) <doi:10.1016/j.celrep.2012.12.008>.

importVCFfiles: Import Mutation data from VCF files.

Description

Usage

Arguments

Value

Details

References