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phers (version 1.0.2)

Calculate Phenotype Risk Scores

Description

Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and rare genetic variants. See Bastarache et al. 2018 .

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Install

install.packages('phers')

Monthly Downloads

256

Version

1.0.2

License

GPL-2

Issues

1

Pull Requests

0

Stars

0

Forks

0

Maintainer

Jake Hughey

Last Published

March 26th, 2023

Functions in phers (1.0.2)

diseaseDxIcdMap

Mapping of diseases and diagnostic ICD codes
getScores

Calculate phenotype risk scores
getResidualScores

Calculate residual phenotype risk scores
getWeights

Calculate phecode-specific weights for phenotype risk scores
getDxStatus

Identify cases and controls for Mendelian diseases
getPhecodeOccurrences

Map ICD code occurrences to phecode occurrences
getGeneticAssociations

Perform association tests between phenotype risk scores and genotypes
mapDiseaseToPhecode

Map diseases to phecodes via HPO terms
icdPhecodeMap

Mapping of ICD codes and phecodes
demoSample

Sample table of demographic information
icdSample

Sample table of ICD occurrences
diseaseHpoMap

Mapping of Mendelian diseases and their clinical features
preCalcWeights

Pre-calculated weights for calculating phenotype risk scores
hpoPhecodeMap

Mapping of HPO terms and phecodes