processVCFdata {mutSignatures} | R Documentation |
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 |
Details
This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.
Value
a data.frame including processed variants from VCF files
Author(s)
Damiano Fantini, damiano.fantini@gmail.com
References
More information and examples about mutational signature analysis can be found here:
-
GitHub Repo: https://github.com/dami82/mutSignatures/
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More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/
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Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/
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Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6