A mapping of diseases to their clinical features, represented as phecodes, is required for calculating phenotype risk scores.
Usage
mapDiseaseToPhecode(
diseaseHpoMap = phers::diseaseHpoMap,
hpoPhecodeMap = phers::hpoPhecodeMap
)Arguments
- diseaseHpoMap
A data.table containing the mapping between diseases and HPO terms. Must have columns
disease_idandterm_id. Default is the map included in this package.- hpoPhecodeMap
A data.table containing the mapping between HPO terms and phecodes. Must have columns
term_idandphecode. Default is the map included in this package.
Examples
library('data.table')
library('survival')
# map ICD codes to phecodes
phecodeOccurrences = getPhecodeOccurrences(icdSample)
# calculate weights using the prevalence method
weightsPrev = getWeights(demoSample, phecodeOccurrences)
# calculate weights using the prevalence method
# (assign negative weights to those with zero phecode occurrence)
weightsPrevNeg = getWeights(
demoSample, phecodeOccurrences, negativeWeights = TRUE)
# calculate weights using the logistic method
weightsLogistic = getWeights(
demoSample, phecodeOccurrences, method = 'logistic', methodFormula = ~ sex)
# calculate weights using the loglinear method
phecodeOccurrences2 = phecodeOccurrences[, .(
num_occurrences = uniqueN(entry_date)), by = .(person_id, phecode)]
weightsLoglinear = getWeights(
demoSample, phecodeOccurrences2, method = 'loglinear', methodFormula = ~ sex)
# calculate weights using the cox method
phecodeOccurrences3 = phecodeOccurrences[, .(
first_occurrence_date = min(entry_date)) , by = .(person_id, phecode)]
phecodeOccurrences3 = merge(
phecodeOccurrences3, demoSample[, .(person_id, dob)], by = 'person_id')
phecodeOccurrences3[,
occurrence_age := as.numeric((first_occurrence_date - dob)/365.25)]
#> person_id phecode first_occurrence_date dob occurrence_age
#> 1: 1 365 2014-03-10 1925-05-24 88.79670
#> 2: 1 366 2014-11-07 1925-05-24 89.45926
#> 3: 1 735 2014-05-28 1925-05-24 89.01299
#> 4: 1 735.1 2014-05-28 1925-05-24 89.01299
#> 5: 2 442 2011-10-10 1976-06-05 35.34601
#> ---
#> 100: 20 531 2017-02-15 2006-09-25 10.39358
#> 101: 20 531.1 2017-02-15 2006-09-25 10.39358
#> 102: 20 661 2019-07-01 2006-09-25 12.76456
#> 103: 20 755 2017-05-10 2006-09-25 10.62356
#> 104: 20 755.3 2017-05-10 2006-09-25 10.62356
phecodeOccurrences3[, `:=`(first_occurrence_date = NULL, dob = NULL)]
#> person_id phecode occurrence_age
#> 1: 1 365 88.79670
#> 2: 1 366 89.45926
#> 3: 1 735 89.01299
#> 4: 1 735.1 89.01299
#> 5: 2 442 35.34601
#> ---
#> 100: 20 531 10.39358
#> 101: 20 531.1 10.39358
#> 102: 20 661 12.76456
#> 103: 20 755 10.62356
#> 104: 20 755.3 10.62356
demoSample3 = demoSample[, .(
person_id, sex,
first_age = as.numeric((first_visit_date - dob)/365.25),
last_age = as.numeric((last_visit_date - dob)/365.25))]
weightsCox = getWeights(
demoSample3, phecodeOccurrences3, method = 'cox', methodFormula = ~ sex)
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
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#> Warning: Ran out of iterations and did not converge
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#> Warning: Ran out of iterations and did not converge
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#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
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#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
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#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
# calculate weights using pre-calculated weights based on data from
# Vanderbilt University Medical Center
weightsPreCalc = getWeights(
demoSample, phecodeOccurrences, method = 'prevalence_precalc')