process.phenotypes: automated phenotype standardization and reporting

Documentation of phenotype cleaning at 54gene

• Overview
• Installation
  • Method 1: Installation from Conda (OSX and Linux only)
  • Method 2: Installation from CRAN
• Execution
  • Environment Setup
  • Run process.phenotypes
• YAML Configuration
  • Top-level YAML Sections
  • Variables YAML Section
  • Derived YAML Section
  • YAML Validation
• Integration with SurveyCTO
  • Retrieve Data from SurveyCTO
  • Convert Forms to process.phenotypes Configurations
  • Expand an Existing process.phenotypes Configuration File for New SurveyCTO Export
• Description of Data Cleaning
  • Load Raw Input Phenotype Data
  • Read in Configuration YAML
  • Drop Invalid Columns
  • Sanitize Header Content in the Input Phenotype Data
  • String Cleanup
  • Apply Consent Exclusions
  • Apply Variable-specific NA Values
  • Apply Type Conversions
  • Exclude Subjects by Age
  • Exclude Subjects Missing Subject IDs
  • Apply Bounds on Numeric Data
  • Attempt to Harmonize Self-reported Ancestry Labels
  • Create Derived Variables
  • Re-apply Bounds on Derived Numeric Variables
  • Check Cross-variable Dependencies
  • Handle Dependency Failures
  • Compute Distribution Data for Numeric Variables
  • Remove Subjects with Excess Invalid Entries Across All Variables
  • Emit an HTML Report
  • Write Out Cleaned Phenotype Data in TSV and/or Various Other Formats
• Variable Types Available
  • About Variable Types
  • Enumerated Variable Types
• Derived Variables
• Helper Functions
• HTML Report
  • Summary and overall metrics
  • Linker table
  • Variable summaries
  • Configuration of Report
• Vignettes
• How to Contribute to Development
  • Step 1: Set up a development environment (OSX and Linux only)
  • Step 2: Select an issue to work on, or submit one that you’d like to address
  • Step 3: Contribute code