bevimed {BeviMed}R Documentation

Bayesian Evaluation of Variant Involvement in Mendelian Disease

Description

Infer probabilities of association between disease label and locus and posterior parameter values under BeviMed model.

Usage

bevimed(
  y,
  G,
  ploidy = rep(2L, length(y)),
  prior_prob_association = 0.01,
  prior_prob_dominant = 0.5,
  dominant_args = NULL,
  recessive_args = NULL,
  ...
)

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.

dominant_args

Arguments to pass to bevimed_m conditioning on dominant inheritance.

recessive_args

Arguments to pass to bevimed_m conditioning on recessive inheritance.

...

Arguments to be passed to bevimed_m for both modes of inheritance.

Value

BeviMed object containing results of inference.

References

Greene et al., A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases, The American Journal of Human Genetics (2017), http://dx.doi.org/10.1016/j.ajhg.2017.05.015.

See Also

prob_association, bevimed_m, summary.BeviMed, bevimed_polytomous


[Package BeviMed version 5.8 Index]