BeviMed: Bayesian Evaluation of Variant Involvement in Mendelian Disorders

A fast integrative genetic association test for rare diseases.

AuthorDaniel Greene
Date of publication2017-02-16 17:27:38
MaintainerDaniel Greene <dg333@cam.ac.uk>
LicenseGPL (>= 2)
Version3.0

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

expected_explained: Get expected number of cases explained by pathogenic...

explaining_variants: Get expected number of variants involved in cases explained...

extract_expected_explained: Extract expected number of cases explained by pathogenic...

extract_explaining_variants: Extract expected number of variants involved in cases...

extract_gamma1_evidence: Extract evidence for gamma = 1 model from 'BeviMed' object.

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...

Functions

bevimed Man page
call_cpp Man page
ccvt Man page
ccvt-package 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_expected_explained Man page
extract_explaining_variants Man page
extract_gamma1_evidence Man page
gamma0_evidence Man page
gamma1_evidence Man page
gamma1_prob Man page
log_BF Man page
lower_bound_gamma1_evidence Man page
print.BeviMed Man page
print.BeviMed_summary Man page
prob_association Man page
prob_pathogenic Man page
region_association_evidence Man page
stack_BeviMeds Man page
stop_chain Man page
summary.BeviMed 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/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/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/extract_gamma1_evidence.Rd BeviMed/man/extract_explaining_variants.Rd BeviMed/man/BeviMed-package.Rd BeviMed/man/expected_explained.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/extract_expected_explained.Rd BeviMed/man/explaining_variants.Rd BeviMed/man/CI_gamma1_evidence.Rd

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