importVCFfiles: Import Mutation data from VCF files.

In dami82/mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Import Mutation data from VCF files.

Description

Import Mutation data from VCF files. The first 8 columns are expected in the following order: c("CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"). Optional columns can be present to inform about sample ID or other info.

Usage

importVCFfiles(vcfFiles, sampleNames = NULL, sampleNameColumn = "SAMPLEID")

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 used as sample identifiers)
sampleNameColumn	string, name of the column that will be added to inform about the sample ID where each variant wes identified

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 column selected via the 'sampleNameColumn' argument.

Author(s)

Damiano Fantini, [e-mail]

References

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

1. Official website: http://www.mutsignatures.org

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

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

dami82/mutSignatures documentation built on Jan. 24, 2023, 12:21 a.m.