grapp Documentation

Contents:

• API Reference
  • Linear Algebra
  • Association Studies (GWAS)
  • Nearest Neighbor Comparisons
  • Filtering, Export, etc.

grapp is a Python library for performing highly scalable, highly efficient calculations on (GRG) files. GRG is a graph-based data structure and file format format. GRG can perform complex data calculations orders of magnitude faster than other methods.

grapp is both a tool set and a framework:

• The tool set includes features like filtering (samples and mutations), PCA, GWAS with covariates, phenotype simulation (via grg_pheno_sim), and data export.

• The framework can be used to build tools/methods for statistical and population genetics. The framework contains Python functionality for integrating GRGs with scipy and other numerical libraries. In particular, the LinearOperator functionality can interoperate with many functions in scipy.sparse.linalg

Both integrate nicely with the Python data analysis ecosystem of numpy, pandas, and scipy.

Indices and tables

• Index

• Module Index

• Search Page