Calculate phenotype risk scoresSource:
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.
A data.table of phecodes and their corresponding weights. Must have columns
A data.table of the mapping between diseases and phecodes. Must have columns
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)