Augment SBS data for mutational signatures deconvolution

Augment a CNAqc object with Single Base Substitution (SBS) data for mutational signature deconvolution.

This creates set of objects that are stored inside field `SBS` of the input object. These are:

* `SNVs`, a tibble for SNVs used for SBS data preparation; * `GRanges`, a GRanges object for the above tibble; * `counts`, a trinucleotide count matrix for SBS deconvolution.

In particular, `counts` is the canonnical format to run SBS deconvolution in a variety of tools.

SBS(x)

Arguments

x

A CNAqc object.

Value

A CNAqc object with required SBS data in the inner field `SBS`.

Examples

if (FALSE) { # \dontrun{
data('example_dataset_CNAqc')
x = init(mutations = example_dataset_CNAqc$mutations, cna =example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)

x = SBS(x)

# All SBS data
print(x$SBS)
} # }