Calculate phenotype risk scores

A person's phenotype risk score for a given disease corresponds to the sum of the weights of the disease-relevant phecodes that the person has received.

Usage

getScores(weights, diseasePhecodeMap)

Arguments

weights

A data.table of phecodes and their corresponding weights. Must have columns person_id, phecode and w.

diseasePhecodeMap

A data.table of the mapping between diseases and phecodes. Must have columns disease_id and phecode.

Value

A data.table containing the phenotype risk score for each person for each disease.

See also

mapDiseaseToPhecode(), getPhecodeOccurrences(), getWeights(), getResidualScores()

Examples

library('data.table')

# map ICD codes to phecodes
phecodeOccurrences = getPhecodeOccurrences(icdSample)

# calculate weights (using the prevalence method)
weights = getWeights(demoSample, phecodeOccurrences)

# OMIM disease IDs for which to calculate phenotype risk scores
diseaseId = 154700

# map diseases to phecodes
diseasePhecodeMap = mapDiseaseToPhecode()

# calculate scores
scores = getScores(weights, diseasePhecodeMap[disease_id == diseaseId])

# calculate residual scores
rscores = getResidualScores(demoSample, scores, lmFormula = ~ sex)