getPhecodeOccurrences: Map ICD code occurrences to phecode occurrences

In phers: Calculate Phenotype Risk Scores

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)

phers documentation built on March 31, 2023, 5:43 p.m.