mutational_signature_effects: Attribute cancer effects to mutational signatures

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

Attribute cancer effects to mutational signatures

Description

Within patients and across the cohort, calculate mutational source probabilities and the share of cancer effects attributable to each source, where sources are biologically-associated mutational signatures. See Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes for background and applications.

Usage

mutational_signature_effects(cesa = cesa, effects = NULL, samples = NULL)

Arguments

cesa	CESAnalysis with cancer effects calculated for the variants of interest.
effects	A table of cancer effect estimates for a set of variants, as produced with ces_variant(). Different sets of variants (or parameter choices in the ces_variant run) will affect output.
samples	Samples for which to calculate mutational sources and effect shares; defaults to all samples. Reported averages apply to the samples included.

Value

A nested list containing...

• mutational_sources (list):

  • source_probabilities (data.table): For each variant in each sample, the probability that each signature was the source of the variant.

  • average_by_variant (data.table): For each distinct variant, the source probabilities averaged over all samples with the variant.

  • average_source_shares (numeric): For each signature, the average proportion of each sample's mutations that are attributable to the signature. Calculated by averaging [CESAnalysis]$mutational_signatures$biological_weights of included samples. Compare with average_effect_shares (described below) to identify signatures with disproportionate contributions to oncogenesis.

• effect_shares (list):

  • by_sample (data.table): The share of each sample's cancer effect (summed across the sample's variants) attributable to each signature.

  • average_effect_shares (numeric): For each signature, the average proportion of each sample's cancer effects that are attributable to signature. Compare with average_source_shares, above, to identify signatures with disproportionate contributions to oncogenesis. Only variants present in effects are included in this calculation.

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