Packaged: 2018-08-17 19:54:27 UTC; cnieuwoudt

Packaged: 2018-10-01 18:11:38 UTC; cnieuwoudt

Packaged: 2020-02-09 19:04:25 UTC; cnieuwoudt

Title: Simulate Genetic Sequence Data for Pedigrees
Description: Methods to simulate genetic sequence data for pedigrees, with
functionality to simulate genetic heterogeneity among pedigrees.
Imports: SimRVPedigree (>= 0.1.0), kinship2 (>= 1.6.4), intervals (>=
Suggests: knitr (>= 1.13), rmarkdown (>= 0.9.6), testthat
Packaged: 2019-03-08 20:09:20 UTC; cnieuwoudt

Packaged: 2019-04-23 22:19:42 UTC; cnieuwoudt

Suggests: knitr (>= 1.13), rmarkdown (>= 0.9.6), vcfR (>= 1.8.0), pryr
Packaged: 2019-11-03 18:08:30 UTC; cnieuwoudt

Packaged: 2019-12-07 17:52:14 UTC; cnieuwoudt

Packaged: 2019-12-30 16:58:18 UTC; cnieuwoudt

Packaged: 2020-03-07 21:04:08 UTC; cnieuwoudt

Packaged: 2020-06-15 01:03:48 UTC; cnieuwoudt

Packaged: 2020-06-28 19:03:28 UTC; cnieuwoudt

Description: Functions for performing Bayesian `similarity regression', adapted to regression of binary genotype against HPO encoded phenotype. The purpose is to weigh the evidence for an association between phenotype and genotype. This is done by estimating a Bayes factor comparing a `no association' model with one in which log odds of presenting a particular binary genotype is linked to the semantic similarity between the corresponding phenotype and an estimated characteristic phenotype.
Imports: Rcpp (>= 0.11.1), dplyr, parallel, ggplot2, plotrix,

Description: Functions for performing Bayesian `similarity regression', adapted to model the association between an HPO-encoded patient phenotype and binary genotype. A `no association' model is compared with one in which the log odds of having a rare genotype is linked to the semantic similarity between patient phenotype and a latent characteristic phenotype. The method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease.

Description: Functions for performing Bayesian `similarity regression',
specialised for modelling the association between a HPO-encoded phenotype
and binary genotype. A `no association' model is compared with one in which
the log odds of having a rare genotype is linked to the semantic similarity
between patient phenotype and a latent characteristic phenotype. The method
estimates the probability of an association together with an HPO-coded phenotype
Imports: Rcpp (>= 0.11.1), ontologyIndex, ontologySimilarity,