create_musica_from_counts: Creates a musica object from a mutation count table

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Creates a musica object from a mutation count table

Description

This function creates a musica object from a mutation count table or matrix. The musica class stores variants information, variant-level annotations, sample-level annotations, and count tables and is used as input to the mutational signature discovery and prediction algorithms.

Usage

create_musica_from_counts(x, variant_class)

Arguments

x	A data.table, matrix, or data.frame that contains counts of mutation types for each sample, with samples as columns.
variant_class	Mutations are SBS, DBS, or Indel.

Value

Returns a musica object

Examples

data(musica)
count_table <- get_count_table(extract_count_tables(musica)$SBS96)
musica <- create_musica_from_counts(count_table, "SBS96")

campbio/musicatk documentation built on Dec. 25, 2024, 9:34 p.m.