Create Multi-Nucleotide Variants (MNVs) counts matrix from input data.
getMNVCounts(data, predefined_dbs_mbs = FALSE)A data.frame with variants having 6 columns: sample name, chromosome, start position, end position, ref, alt.
Boolean. As defined by the function get_mut_type from the package MutationalPatterns, it specifies whether dbs and mbs mutations have been predefined in the input data. This function by default assumes that dbs and mbs mutations are present in the vcf as snvs, which are positioned next to each other. If your dbs/mbs mutations are called separately, you should set this argument to TRUE.
A matrix with Multi-Nucleotide Variants (MNVs) counts per patient.
data(ssm560_reduced)
res <- getMNVCounts(data = ssm560_reduced)
#> Any neighbouring SNVs will be merged into DBS/MBS variants.
#> Set the 'predefined_dbs_mbs' to 'TRUE' if you don't want this.
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