clean_process_clinical_data: Clean and process EHR data

In pwatrick/DrugRepurposingToolKit: A High-Throughput Approach Integrating Gene Expression Signatures and Clinical Data to Repurpose Drugs

Clean and process EHR data

Description

clean_process_clinical_data cleans and processes clinical EHR data.

Usage

clean_process_clinical_data(
  drug,
  phenotype,
  biomarker,
  indication_drugs,
  concept_id_exclusions,
  r_covariates,
  r_drugs,
  r_biomarkers
)

Arguments

drug	A string, e.g., "simvastatin"
phenotype	A string, e.g., "Hyperlipidemia"
biomarker	A string, e.g., "LDL Cholesterol"
indication_drugs	A tibble with columns c('rxcui_in', 'drug_desc', 'indication'), eg, DrugRepurposingToolKit::drugsHyperlipidemia
concept_id_exclusions	A vector, e.g., c(2212451). Used for excluding concept_ids which may not contain the correct values
r_covariates	A tibble with columns c('person_id','dob','gender_concept_id', 'race_concept_id', drug_concept_id', 'first_drug_exposure','last_drug_exposure')
r_drugs	A tibble with columns c('person_id','start_date','end_date', 'drug_exposure_start_date','drug_concept_id')
r_biomarkers	A tibble with columns c('person_id','start_date','measurement_date', 'end_date', 'measurement_concept_id', 'value_as_number')

Details

This function cleans and processes clinical data from electronic health record (EHR) databases that have adopted the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) format.

Updated: 2021-03-27

pwatrick/DrugRepurposingToolKit documentation built on Aug. 10, 2024, 7:12 a.m.