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Attribute cancer effects to mutational signatures

Source: R/mutational_signature_effects.R
mutational_signature_effects.Rd

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.