analyze_clinical_data: Processes clinical data and outputs table summarizing...

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

Description

Processes clinical data and outputs table summarizing treatment effect and number of overlapping patients in raw data Last updated: 2021-02-17

Usage

analyze_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.