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 characteristic of the disease.
| Version: | 1.3 |
| Depends: | R (≥ 3.0.0) |
| Imports: | Rcpp (≥ 0.11.1), ontologyIndex, ontologySimilarity, ontologyPlot, plotrix |
| LinkingTo: | Rcpp |
| Suggests: | knitr |
| Published: | 2016-01-13 |
| Author: | Daniel Greene |
| Maintainer: | Daniel Greene <dg333 at cam.ac.uk> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | yes |
| CRAN checks: | SimReg results |
| Reference manual: | SimReg.pdf |
| Vignettes: |
Similarity Regression |
| Package source: | SimReg_1.3.tar.gz |
| Windows binaries: | r-devel: SimReg_1.3.zip, r-release: SimReg_1.3.zip, r-oldrel: SimReg_1.3.zip |
| OS X Snow Leopard binaries: | r-release: not available, r-oldrel: not available |
| OS X Mavericks binaries: | r-release: SimReg_1.3.tgz |
| Old sources: | SimReg archive |