View source: R/run_mutational_patterns.R
run_mutational_patterns | R Documentation |
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.
run_mutational_patterns(
tumor_trinuc_counts,
signatures_df,
signatures_to_remove,
mp_strict_args = list(),
bootstrap_mutations = FALSE
)
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(). |
a data.frame of signature weights
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