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 |

**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...

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
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.