Overview

Phenofhy provides a small set of building blocks for OFH phenotype work:

• Extraction: build a field list and extract data from DNAnexus datasets.
• Processing: derive common variables and clean fields by entity.
• Calculation: produce summary and prevalence tables.
• Profiling: generate a basic phenotype profile report.

Phenofhy is designed primarily for OFH TRE workflows, but key processing and analysis steps can also be tested locally using simulated data.

The package is organized by module, with each module focused on one stage of the workflow. The API reference is grouped the same way.