Estimation of Neutral Mutation Rates and Quantification of Somatic Variant Selection Using cancereffectsizeR.

ABSTRACT: Somatic nucleotide mutations can contribute to cancer cell survival, proliferation, and pathogenesis. Although research has focused on identifying which mutations are "drivers" versus "passengers," quantifying the proliferative effects of specific variants within clinically relevant contexts could reveal novel aspects of cancer biology. To enable researchers to estimate these cancer effects, we developed cancereffectsizeR, an R package that organizes somatic variant data, facilitates mutational signature analysis, calculates site-specific mutation rates, and tests models of selection. Built-in models support effect estimation from single nucleotides to genes. Users can also estimate epistatic effects between paired sets of variants, or design and test custom models. The utility of cancer e

SUBMITTER: Mandell JD 

PROVIDER: S-EPMC9929515 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature