Package: phers 1.0.2
Jake Hughey
phers: Calculate Phenotype Risk Scores
Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and rare genetic variants. See Bastarache et al. 2018 <doi:10.1126/science.aal4043>.
Authors:
phers_1.0.2.tar.gz
phers_1.0.2.zip(r-4.5)phers_1.0.2.zip(r-4.4)phers_1.0.2.zip(r-4.3)
phers_1.0.2.tgz(r-4.4-any)phers_1.0.2.tgz(r-4.3-any)
phers_1.0.2.tar.gz(r-4.5-noble)phers_1.0.2.tar.gz(r-4.4-noble)
phers_1.0.2.tgz(r-4.4-emscripten)phers_1.0.2.tgz(r-4.3-emscripten)
phers.pdf |phers.html✨
phers/json (API)
NEWS
| # Install 'phers' in R: |
| install.packages('phers', repos = c('https://hugheylab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hugheylab/phers/issues
- demoSample - Sample table of demographic information
- diseaseDxIcdMap - Mapping of diseases and diagnostic ICD codes
- diseaseHpoMap - Mapping of Mendelian diseases and their clinical features
- hpoPhecodeMap - Mapping of HPO terms and phecodes
- icdPhecodeMap - Mapping of ICD codes and phecodes
- icdSample - Sample table of ICD occurrences
- preCalcWeights - Pre-calculated weights for calculating phenotype risk scores
Last updated 2 years agofrom:60afad7fb3. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-win | OK | Nov 01 2024 |
| R-4.5-linux | OK | Nov 01 2024 |
| R-4.4-win | OK | Nov 01 2024 |
| R-4.4-mac | OK | Nov 01 2024 |
| R-4.3-win | OK | Nov 01 2024 |
| R-4.3-mac | OK | Nov 01 2024 |
Exports:getDxStatusgetGeneticAssociationsgetPhecodeOccurrencesgetResidualScoresgetScoresgetWeightsmapDiseaseToPhecode
Dependencies:backportsBEDMatrixcheckmatecodetoolscrochetdata.tableforeachiteratorslatticeMatrixsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Sample table of demographic information | demoSample |
| Mapping of diseases and diagnostic ICD codes | diseaseDxIcdMap |
| Mapping of Mendelian diseases and their clinical features | diseaseHpoMap |
| Identify cases and controls for Mendelian diseases | getDxStatus |
| Perform association tests between phenotype risk scores and genotypes | getGeneticAssociations |
| Map ICD code occurrences to phecode occurrences | getPhecodeOccurrences |
| Calculate residual phenotype risk scores | getResidualScores |
| Calculate phenotype risk scores | getScores |
| Calculate phecode-specific weights for phenotype risk scores | getWeights |
| Mapping of HPO terms and phecodes | hpoPhecodeMap |
| Mapping of ICD codes and phecodes | icdPhecodeMap |
| Sample table of ICD occurrences | icdSample |
| Map diseases to phecodes via HPO terms | mapDiseaseToPhecode |
| Pre-calculated weights for calculating phenotype risk scores | preCalcWeights |
