clean_process_clinical_data: Cleans and processes clinical data extracted from EHR...

In pwatrick/systematicRepurposing: Integrates Transriptomics and Clinical Data to Identify Drug Repurposing Candidates

Description

Cleans and processes clinical data extracted from EHR formatted in OHDSI/OMOP CDM. Output is a tibble with each row representing one patient. This function was created to create tibble with only patients not exposed to known approve drugs for the phenotype of interest, besides the drug being tested, ie, if "simvastatin" is being tested for its effect on treating hyperlipidemia, "simvastatin" would be removed from the indication drug list, but other statins would still remain. Last updated: 2021-03-13

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'), e.g., systematicRepurposing::lipid_drugs_20201217141539
concept_id_exclusions	A vector, e.g., c(2212451)
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')

pwatrick/systematicRepurposing documentation built on March 24, 2021, 5:49 p.m.