BeviMed (version 3.0)

prob_pathogenic: Calculate probability of pathogencity for variants in region given a prior probability of association between case label and the region

Description

Calculate probability of pathogencity for variants in region given a prior probability of association between case label and the region

Usage

prob_pathogenic(y, G, ploidy = rep(2L, length(y)),
  prior_prob_association = 0.01, prior_prob_dominant = 0.5,
  tau0_shape = c(1, 1), by_MOI = FALSE, ...)

Arguments

y

Logical vector of case (TRUE) control (FALSE) status.

G

Integer matrix of variant counts per individual, one row per individual and one column per variant.

ploidy

Integer vector giving ploidy of samples.

prior_prob_association

The prior probability of association.

prior_prob_dominant

The prior probability of dominant inheritance given that there is an association.

tau0_shape

Beta shape hyper-priors for prior on rate of case labels.

by_MOI

Logical value determining whether to return probabilities broken down by mode of inheritance.

...

Other arguments to pass to bevimed.

Value

Probabilities of pathogenicity.