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API Reference

Data Structures

  • GWADataLoader: A general class for loading multiple statistical genetics data sources and harmonizing them for downstream analyses.
  • GenotypeMatrix: A common interface for PLINK BED-backed genotype matrices, with implementations for the native magenpy, bed-reader, plink, and xarray backends.
  • LDMatrix: A class for representing on-disk Linkage-Disequilibrium (LD) matrices. It provides interfaces for querying / manipulating / and performing computations on LD data.
  • SampleTable: A class for representing data about samples (individuals), including covariates, phenotypes, and other sample-specific metadata.
  • SumstatsTable: A class for representing summary statistics data from a GWAS study. It provides interfaces for querying / manipulating / and performing computations on summary statistics data.
  • AnnotationMatrix: A class for representing variant annotations (e.g. functional annotations, pathogenicity scores, etc.) for a set of variants. It provides interfaces for querying / manipulating / and performing computations on annotation data.

Simulation

Parsers

  • Sumstats Parsers: A collection of parsers for reading GWAS summary statistics files in various formats.
  • Annotation Parsers: A collection of parsers for reading variant annotation files in various formats.
  • Plink Parsers: A collection of parsers for reading PLINK files (BED/BIM/FAM) and other PLINK-related formats.

Statistics

Plotting

  • GWAS plots: Functions for plotting various quantities / results from GWAS studies.
  • LD plots: Functions for plotting various quantities from LD matrices.

Utilities

  • Compute utilities: Utilities for computing various statistics / quantities over python data structures.
  • Data utilities: Utilities for downloading and processing relevant data.
  • Executors: A collection of classes for interfacing with third party software, such as plink.
  • Model utilities: Utilities for merging / aligning / filtering GWAS data sources.
  • System utilities: Utilities for interfacing with the system environment (e.g. file I/O, environment variables, etc.).

Data