getPhecodeOccurrences {phers}

Map ICD code occurrences to phecode occurrences

Description

This is typically the first step of an analysis using phenotype risk scores, the next is getWeights().

Usage

getPhecodeOccurrences(
  icdOccurrences,
  icdPhecodeMap = phers::icdPhecodeMap,
  dxIcd = phers::diseaseDxIcdMap
)

Arguments

icdOccurrences

A data.table of occurrences of ICD codes for each person in the cohort. Must have columns person_id, icd, and flag.

icdPhecodeMap

A data.table of the mapping between ICD codes and phecodes. Must have columns icd, phecode, and flag. Default is the map included in this package.

dxIcd

A data.table of ICD codes to exclude from mapping to phecodes. Must have columns icd and flag. Default is the table of Mendelian diseases and the corresponding ICD codes that indicate a genetic diagnosis. If NULL, no ICD codes will be excluded.

Value

A data.table of phecode occurrences for each person.

See Also

getWeights(), getScores()

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)