# 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.

## 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.