process_biomarker: Process biomarkers data

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

Process biomarkers data

Description

process_biomarker sets up biomarkers for hypothesis testing

Usage

process_biomarker(
  biomarker_tbl,
  biomarker_name,
  covariates_flagged,
  baseline_cols,
  inclusion_cols,
  concept_id_exclusions,
  ...
)

Arguments

biomarker_tbl	A tibble with columns, c('person_id','start_date','measurement_date', 'end_date','measurement_concept_id', 'value_as_number')
biomarker_name	A string, e.g., "LDL cholesterol"
covariates_flagged	A tibble with columns, c('person_id','dob','gender_concept_id', 'race_concept_id','start_date', 'first_drug_exposure','final_end_date','age', 'drug_exposed','treatment_new_exposed')
baseline_cols	A vector, e.g. c('person_id', 'start_date', 'first_drug_exposure', 'final_end_date')
inclusion_cols	A vector, e.g., c('person_id', 'measurement_date', 'measurement_concept_id', 'value_as_number')
concept_id_exclusions	A vector, e.g., for LDL, c(2212451)

Details

This function sets up biomarkers for hypothesis testing. Updated: 2021-03-27

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