extract_clinical_data: Extract clinical data from All of Us dataset

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

Extract clinical data from All of Us dataset

Description

extract_clinical_data creates SQL query to extract clinical EHR data from All of Us dataset

Usage

extract_clinical_data(
  drug_concept_id,
  biomarker_concept_id,
  table_name,
  table_type,
  indication_drug_concept_ids
)

Arguments

drug_concept_id	A string, indicating drug RxNorm ingredient OHDSI concept_id, eg, "1332418" for amlodipine
biomarker_concept_id	A string, indicating biomarker's OHDSI concept_id, eg, "3004249" for Systolic Blood Pressure
table_name	A string, indicating
table_type	A string, either c("covariates", "drugs", "biomarkers")
indication_drug_concept_ids	A string, with concept_ids for indication drugs, eg, for lipid-lowering drugs: "(drug_concept_id,1551803,19011061, 1351115,1558242,19004048,19051463, 19018419,1510813,1501617,1592085,1545958, 1549686,46275447,1551860,19082770,1586226, 19095309,46274162,957797,1517824,46287466, 19022956,40165636,1518148,19026600,1539403 ,1526475)"

Details

Updated: 2021-03-27

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