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BeviMed (version 1.2)

Bayesian Evaluation of Variant Involvement in Mendelian Disorders

Description

Bayesian inference procedures for evaluating evidence of involvement of variants in Mendelian disorders based on intuitive models of dominant and recessive inheritance.

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Version

Install

install.packages('BeviMed')

Monthly Downloads

658

Version

1.2

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

May 3rd, 2016

Functions in BeviMed (1.2)

log P_r

Calculate marginal probability of observed genotypes under 'pathogenic region' model

lower_bound_P_v_by_direct_sum

Calculate marginal probability of observed genotypes under variant-level pathogenicity model by summing over marginals condintional on pathogenic variant combinations

probability_pathogenic

Calculate region or variant-level probability of pathogencity given prior probability on pathogenicity of region

stack_BeviMeds

Concatenate objects of class BeviMed

call_cpp

R interface to BeviMed c++ MCMC procedure

log P_v

Calculate marginal probability of observed genotypes under variant-level pathogenicity model

stop_chain

Apply the MCMC algorithm in blocks until conditions are met

bevimed

Perform inference under model variant-level model v for y using MCMC sampling

sample_posterior_v

Generate samples from the posterior under the variant-level pathogenicity model

tune_temperatures

Tune temperatures using interval bisection to minimimise Kullback-Liebler divergence between adjacent power posteriors

log P_n

Calculate marginal probability of observed genotypes under 'null' model

ccvt-package

A short title line describing what the package does

print.BeviMed_summary

Print readable summary of BeviMed_summary object.

log BF

Calculate log Bayes factor comparing the variant-level model for case-control status

estimate_confidence_interval

Estimate confidence interval for estimated marginal likelihood by simulation

power_posteriors_ML_sum

Calculate the Marginal Likelihood under v by summation over power posterior likelihood exptectances

print.BeviMed

Print readable summary of BeviMed object.

tune_proposal_sds

Tune the proposal standard deviations for the Metropolis-Hastings updates of either phi or omega

summary.BeviMed

Create summary of BeviMed classed-object