BeviMed: Bayesian Evaluation of Variant Involvement in Mendelian Disease
Version 5.0

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.

AuthorDaniel Greene, Sylvia Richardson and Ernest Turro
Date of publication2017-04-22 16:21:07 UTC
MaintainerDaniel Greene <dg333@cam.ac.uk>
LicenseGPL (>= 2)
Version5.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BeviMed")

Getting started

Package overview
BeviMed Introduction
BeviMed with VCFs

Popular man pages

bevimed_m: Perform inference under model gamma = 1 conditional on mode...
BeviMed-package: Bayesian Evaluation of Variant Involvement in Mendelian...
expected_explained: Calculate expected number of explained cases
extract_conditional_prob_pathogenic: Extract probability of pathogenicity for variant conditional...
gamma1_evidence: Calculate evidence under model gamma = 1
print.BeviMed: Print readable summary of 'BeviMed' object
prob_association: Calculate probability of association
See all...

All man pages Function index File listing

Man pages

bevimed: Bayesian Evaluation of Variant Involvement in Mendelian...
bevimed_m: Perform inference under model gamma = 1 conditional on mode...
BeviMed-package: Bayesian Evaluation of Variant Involvement in Mendelian...
bevimed_polytomous: Model selection for multiple association models
call_cpp: R interface to BeviMed c++ MCMC procedure
CI_gamma1_evidence: Estimate confidence interval for estimated marginal...
conditional_prob_pathogenic: Calculate probability of pathogencity for variants...
exact_evidence: Calculate exact evidence for model gamma = 1
expected_explained: Calculate expected number of explained cases
explaining_variants: Calculate expected number of pathogenic variants in cases
extract_conditional_prob_pathogenic: Extract probability of pathogenicity for variant conditional...
extract_expected_explained: Extract expected number of explained cases
extract_explaining_variants: Extract expected number of pathogenic variants in cases
extract_gamma1_evidence: Extract evidence for model gamma = 1
extract_prob_association: Extract the posterior probability of association
extract_prob_pathogenic: Extract variant marginal probabilities of pathogenicity
gamma0_evidence: Calculate marginal probability of observed case-control...
gamma1_evidence: Calculate evidence under model gamma = 1
log_BF: Calculate log Bayes factor between an association model with...
lower_bound_gamma1_evidence: Calculate log lower bound for marginal probability under...
print.BeviMed: Print readable summary of 'BeviMed' object
print.BeviMed_m: Print 'BeviMed_m' object
print.BeviMed_summary: Print readable summary of 'BeviMed_summary' object.
prob_association: Calculate probability of association
prob_association_m: Calculate probability of association for one mode of...
prob_pathogenic: Calculate variant marginal probabilities of pathogencity
region_association_evidence: Calculate evidence of under pathogenic locus model
stack_BeviMeds: Concatenate objects of class 'BeviMed_raw'
stop_chain: Apply the MCMC algorithm in blocks until conditions are met
summary.BeviMed: Summarise a 'BeviMed' object
summary.BeviMed_m: Summarise a 'BeviMed_m' object
sum_ML_over_PP: Calculate marginal likelihood from power posteriors output
tune_proposal_sds: Tune proposal standard deviation for MH sampled parameters
tune_temperatures: Tune temperatures

Functions

BeviMed Man page
BeviMed-package Man page
CI_gamma1_evidence Man page Source code
bevimed Man page Source code
bevimed_m Man page Source code
bevimed_mc Source code
bevimed_polytomous Man page Source code
call_cpp Man page Source code
conditional_prob_pathogenic Man page Source code
exact_evidence Man page Source code
expected_explained Man page Source code
explaining_variants Man page Source code
extract_conditional_prob_pathogenic Man page Source code
extract_expected_explained Man page Source code
extract_explaining_variants Man page Source code
extract_gamma1_evidence Man page Source code
extract_prob_association Man page Source code
extract_prob_pathogenic Man page Source code
gamma0_evidence Man page Source code
gamma1_evidence Man page Source code
get_G_args Source code
log_BF Man page Source code
lower_bound_gamma1_evidence Man page Source code
print.BeviMed Man page Source code
print.BeviMed_m Man page Source code
print.BeviMed_summary Man page Source code
prob_association Man page Source code
prob_association_m Man page Source code
prob_pathogenic Man page Source code
region_association_evidence Man page Source code
stack_BeviMeds Man page Source code
stop_chain Man page Source code
sum_ML_over_PP Man page Source code
summary.BeviMed Man page Source code
summary.BeviMed_m Man page Source code
to_var_tab Source code
tune_proposal_sds Man page Source code
tune_temperatures Man page Source code
variant_marginals Source code

Files

inst
inst/scripts
inst/scripts/vcf.R
inst/doc
inst/doc/vcf.html
inst/doc/Intro.R
inst/doc/Intro.Rmd
inst/doc/vcf.R
inst/doc/vcf.Rmd
inst/doc/Intro.html
inst/doc/Guide.Rnw
inst/doc/Guide.pdf
inst/doc/Guide.R
src
src/BeviMed_init.c
src/sampling.h
src/sampling.cpp
src/RcppExports.cpp
NAMESPACE
NEWS.md
R
R/convenience.R
R/generics.R
R/functions.R
R/RcppExports.R
vignettes
vignettes/Intro.Rmd
vignettes/vcf.Rmd
vignettes/Guide.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/call_cpp.Rd
man/bevimed_m.Rd
man/extract_conditional_prob_pathogenic.Rd
man/stop_chain.Rd
man/exact_evidence.Rd
man/sum_ML_over_PP.Rd
man/region_association_evidence.Rd
man/gamma0_evidence.Rd
man/print.BeviMed_m.Rd
man/log_BF.Rd
man/prob_pathogenic.Rd
man/extract_prob_association.Rd
man/conditional_prob_pathogenic.Rd
man/summary.BeviMed.Rd
man/prob_association.Rd
man/lower_bound_gamma1_evidence.Rd
man/print.BeviMed_summary.Rd
man/print.BeviMed.Rd
man/extract_gamma1_evidence.Rd
man/extract_explaining_variants.Rd
man/BeviMed-package.Rd
man/expected_explained.Rd
man/extract_prob_pathogenic.Rd
man/prob_association_m.Rd
man/tune_proposal_sds.Rd
man/gamma1_evidence.Rd
man/summary.BeviMed_m.Rd
man/bevimed_polytomous.Rd
man/stack_BeviMeds.Rd
man/tune_temperatures.Rd
man/bevimed.Rd
man/extract_expected_explained.Rd
man/explaining_variants.Rd
man/CI_gamma1_evidence.Rd
BeviMed documentation built on May 19, 2017, 8:02 p.m.

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