pairwise_variant_epistasis: Estimate selection under pairwise epistasis model

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

Estimate selection under pairwise epistasis model

Description

Estimate selection under pairwise epistasis model

Usage

pairwise_variant_epistasis(
  cesa,
  variant_pair,
  samples,
  conf,
  compound_variants = NULL,
  model = "default",
  lik_args = list(),
  optimizer_args = list(),
  pval_calc_fn = NULL
)

Arguments

cesa	CESAnalysis
variant_pair	2-length character of variant IDs, or 2-length numeric giving indices of CompoundVariantSet for the current two compound variants
samples	Validated samples data.table (as from select_samples())
compound_variants	If testing a pair of compound variants, the CompoundVariantSet defining them
model	Passed from ces_epistasis or ces_gene_epistasis. Set to "default" to use built-in model of epistatic selection, or supply a custom function factory (see details).
lik_args	Extra arguments, given as a list, passed from ces_epistasis or ces_gene_epistasis
optimizer_args	List of arguments to pass to the optimizer (bbmle::mle2).
pval_calc_fn	For use with custom models; optional. A function that takes an epistasis model fit as input and returns p-values and other descriptives.

Townsend-Lab-Yale/cancereffectsizeR documentation built on Feb. 15, 2025, 10:23 a.m.