run_deconstructSigs: cancereffectsizeR wrapper for deconstructSigs

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

cancereffectsizeR wrapper for deconstructSigs

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 a data.frame of signature weights.

Usage

run_deconstructSigs(
  tumor_trinuc_counts,
  signatures_df,
  signatures_to_remove,
  tri.counts.method
)

Arguments

tumor_trinuc_counts	one-row data.frame of trinuc variant counts (in deconstructSigs order) for one tumor
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 deconstructSigs and assign zero weights
tri.counts.method	exome/genome trinucleotide content normalization argument to pass to deconstructSigs (see its docs)

Value

a data.frame of signature weights

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