SBS: Augment SBS data for mutational signatures deconvolution

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

Augment SBS data for mutational signatures deconvolution

Description

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.

Usage

SBS(x)

Arguments

x	A CNAqc object.

Value

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

Examples

## Not run: 
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)

## End(Not run)

caravagnalab/CNAqc documentation built on Feb. 28, 2025, 12:08 p.m.