run_mutational_patterns: cancereffectsizeR wrapper for fit_to_signatures

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

cancereffectsizeR wrapper for fit_to_signatures

Description

This function gets called internally by trinuc_mutation_rates() for each tumor in a CESAnalysis, accepting a data.frame of mutation counts and returning fit_to_signatures output. Note: this function supports indels if passed in the same format.

Usage

run_mutational_patterns(
  tumor_trinuc_counts,
  signatures_df,
  signatures_to_remove,
  mp_strict_args = list(),
  bootstrap_mutations = FALSE
)

Arguments

tumor_trinuc_counts	matrix of trinuc variant counts where columns respond to tumors and order of trinucleotide changes match signatures_df
signatures_df	data.frame of signatures (see COSMIC v3 signatures included with package for format)
signatures_to_remove	names of signatures in signatures_df to keep out of MutationalPatterns and assign zero weights. Only occurs when strict == FALSE
mp_strict_args	named list of additional arguments to fit_to_signatures_strict
bootstrap_mutations	T/F (default FALSE) whether to run fit_to_signatures_bootstrapped() with n_boot = 1 instead of fit_to_signatures_strict().

Value

a data.frame of signature weights

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.