BeviMed: Bayesian Evaluation of Variant Involvement in Mendelian Disorders

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

Author
Daniel Greene
Date of publication
2016-07-05 23:43:22
Maintainer
Daniel Greene <dg333@cam.ac.uk>
License
GPL (>= 2)
Version
2.2

View on CRAN

Man pages

bevimed
Perform inference under model gamma = 1
BeviMed-package
A short title line describing what the package does
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 in region...
exact_evidence
Calculate exact evidence for model gamma=1
gamma0_evidence
Calculate marginal probability of observed case-control...
gamma1_evidence
Calculate marginal probability of observed case-control...
gamma1_prob
Calculate probability of an association
log_BF
Calculate log Bayes factor between models gamma=1 and gamma=0...
lower_bound_gamma1_evidence
Calculate log lower bound for marginal probability of...
print.BeviMed
Print readable summary of 'BeviMed' object.
print.BeviMed_summary
Print readable summary of 'BeviMed_summary' object.
prob_association
Calculate probability of an association between...
prob_pathogenic
Calculate probability of pathogencity for variants in region...
region_association_evidence
Calculate marginal probability of observed genotypes under...
stack_BeviMeds
Concatenate objects of class 'BeviMed'
stop_chain
Apply the MCMC algorithm in blocks until conditions are met
summary.BeviMed
Create summary of 'BeviMed' classed-object
sum_ML_over_PP
Calculate the Marginal Likelihood by summation over power...
tune_proposal_sds
Tune the proposal standard deviations for the...
tune_temperatures
Tune temperatures using interval bisection to minimimise...

Files in this package

BeviMed
BeviMed/inst
BeviMed/inst/scripts
BeviMed/inst/scripts/bevimed-vcf.R
BeviMed/inst/doc
BeviMed/inst/doc/Intro.R
BeviMed/inst/doc/Intro.Rmd
BeviMed/inst/doc/Intro.html
BeviMed/src
BeviMed/src/sampling.h
BeviMed/src/sampling.cpp
BeviMed/src/RcppExports.cpp
BeviMed/src/RcppExports.h
BeviMed/NAMESPACE
BeviMed/R
BeviMed/R/generics.R
BeviMed/R/functions.R
BeviMed/vignettes
BeviMed/vignettes/Intro.Rmd
BeviMed/MD5
BeviMed/build
BeviMed/build/vignette.rds
BeviMed/DESCRIPTION
BeviMed/man
BeviMed/man/call_cpp.Rd
BeviMed/man/stop_chain.Rd
BeviMed/man/exact_evidence.Rd
BeviMed/man/sum_ML_over_PP.Rd
BeviMed/man/region_association_evidence.Rd
BeviMed/man/gamma0_evidence.Rd
BeviMed/man/log_BF.Rd
BeviMed/man/prob_pathogenic.Rd
BeviMed/man/conditional_prob_pathogenic.Rd
BeviMed/man/summary.BeviMed.Rd
BeviMed/man/prob_association.Rd
BeviMed/man/lower_bound_gamma1_evidence.Rd
BeviMed/man/print.BeviMed_summary.Rd
BeviMed/man/print.BeviMed.Rd
BeviMed/man/BeviMed-package.Rd
BeviMed/man/tune_proposal_sds.Rd
BeviMed/man/gamma1_evidence.Rd
BeviMed/man/stack_BeviMeds.Rd
BeviMed/man/tune_temperatures.Rd
BeviMed/man/gamma1_prob.Rd
BeviMed/man/bevimed.Rd
BeviMed/man/CI_gamma1_evidence.Rd