prob_pathogenic

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

by_model

Arguments to pass to <code><a rd-options="" href="/link/bevimed?package=BeviMed&version=5.8" data-mini-rdoc="BeviMed::bevimed">bevimed</a></code>.

Calls <code><a rd-options="" href="/link/bevimed?package=BeviMed&version=5.8" data-mini-rdoc="BeviMed::bevimed">bevimed</a></code> and <code><a rd-options="" href="/link/extract_prob_pathogenic?package=BeviMed&version=5.8" data-mini-rdoc="BeviMed::extract_prob_pathogenic">extract_prob_pathogenic</a></code> to obtain marginal probabilities of pathogenicity.

A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework - 'A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases', Greene et al 2017 <doi:10.1016/j.ajhg.2017.05.015>.

Daniel Greene

BeviMed

Bayesian Evaluation of Variant Involvement in Mendelian Disease

prob_pathogenic function

Arguments to pass to <code><a rd-options='' href='bevimed'>bevimed</a></code>.

Calls <code><a rd-options='' href='bevimed'>bevimed</a></code> and <code><a rd-options='' href='extract_prob_pathogenic'>extract_prob_pathogenic</a></code> to obtain marginal probabilities of pathogenicity.

prob_pathogenic: Calculate variant marginal probabilities of pathogencity

Description

Usage

Arguments

Value

See Also