Attribute cancer effects to mutational signaturesSource:
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.
CESAnalysis with cancer effects calculated for the variants of interest.
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_variantrun) will affect output.
Samples for which to calculate mutational sources and effect shares; defaults to all samples. Reported averages apply to the samples included.
A nested list containing...
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_weightsof included samples. Compare with average_effect_shares (described below) to identify signatures with disproportionate contributions to oncogenesis.
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): Across the cohort, the average share of cancer effect attributable to each signature. Compare with average_source_shares, above, to identify signatures with disproportionate contributions to oncogenesis.