BeviMed: Bayesian Evaluation of Variant Involvement in Mendelian Disease

A fast integrative genetic association test for rare diseases.

AuthorDaniel Greene
Date of publication2017-03-01 08:36:15
MaintainerDaniel Greene <dg333@cam.ac.uk>
LicenseGPL (>= 2)
Version4.0

View on CRAN

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...

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 model gamma = 1...

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

Files

BeviMed
BeviMed/inst
BeviMed/inst/scripts
BeviMed/inst/scripts/vcf.R
BeviMed/inst/doc
BeviMed/inst/doc/vcf.html
BeviMed/inst/doc/Intro.R
BeviMed/inst/doc/Intro.Rmd
BeviMed/inst/doc/vcf.R
BeviMed/inst/doc/vcf.Rmd
BeviMed/inst/doc/Intro.html
BeviMed/inst/doc/Guide.Rnw
BeviMed/inst/doc/Guide.pdf
BeviMed/inst/doc/Guide.R
BeviMed/src
BeviMed/src/BeviMed_init.c
BeviMed/src/sampling.h
BeviMed/src/sampling.cpp
BeviMed/src/RcppExports.cpp
BeviMed/NAMESPACE
BeviMed/NEWS.md
BeviMed/R
BeviMed/R/convenience.R BeviMed/R/generics.R BeviMed/R/functions.R BeviMed/R/RcppExports.R
BeviMed/vignettes
BeviMed/vignettes/Intro.Rmd
BeviMed/vignettes/vcf.Rmd
BeviMed/vignettes/Guide.Rnw
BeviMed/MD5
BeviMed/build
BeviMed/build/vignette.rds
BeviMed/DESCRIPTION
BeviMed/man
BeviMed/man/call_cpp.Rd BeviMed/man/bevimed_m.Rd BeviMed/man/extract_conditional_prob_pathogenic.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/print.BeviMed_m.Rd BeviMed/man/log_BF.Rd BeviMed/man/prob_pathogenic.Rd BeviMed/man/extract_prob_association.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/extract_gamma1_evidence.Rd BeviMed/man/extract_explaining_variants.Rd BeviMed/man/BeviMed-package.Rd BeviMed/man/expected_explained.Rd BeviMed/man/extract_prob_pathogenic.Rd BeviMed/man/prob_association_m.Rd BeviMed/man/tune_proposal_sds.Rd BeviMed/man/gamma1_evidence.Rd BeviMed/man/summary.BeviMed_m.Rd BeviMed/man/stack_BeviMeds.Rd BeviMed/man/tune_temperatures.Rd BeviMed/man/bevimed.Rd BeviMed/man/extract_expected_explained.Rd BeviMed/man/explaining_variants.Rd BeviMed/man/CI_gamma1_evidence.Rd

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