processVCFdata: Process VCF data.

Description

Check, annotate, and process variants imported from a list of VCF files, so that it can be used to run a mutational signature analysis

Usage

processVCFdata(
  vcfData,
  BSGenomeDb,
  chr_colName = "CHROM",
  pos_colName = "POS",
  ref_colName = "REF",
  alt_colName = "ALT",
  sample_colName = NULL,
  nucl_contextN = 3,
  verbose = TRUE
)

Arguments

vcfData

data.frame, includes mutation data from 2 or more samples

BSGenomeDb

a BSGenomeDb-class object storing the genomic sequences and coordinates

chr_colName

string, name of the column including the chromosome (seq) name. Defaults to "CHROM"

pos_colName

string, name of the column including the genomic coordinates/position. Defaults to "POS"

ref_colName

string, name of the column including the reference nucleotide. Defaults to "REF"

alt_colName

string, name of the column including the variant nucleotide. Defaults to "ALT"

sample_colName

string, name of the column including the sample ID. Can be NULL

nucl_contextN

integer, span (in nucelotides) of the context around the variants. Defaults to 3

verbose

logical, shall information about the ongoing analysis be printed to console

Value

a data.frame including processed variants from VCF files

Details

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

References

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

GitHub Repo: https://github.com/dami82/mutSignatures/
More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/
Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/
Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6