PascalX: a Python library for GWAS gene and pathway enrichment tests

Daniel Krefl; Alessandro Brandulas Cammarata; Sven Bergmann

doi:10.1093/bioinformatics/btad296

PascalX: a Python library for GWAS gene and pathway enrichment tests

Bioinformatics. 2023 May 4;39(5):btad296. doi: 10.1093/bioinformatics/btad296.

Authors

Daniel Krefl^{1

2}, Alessandro Brandulas Cammarata¹, Sven Bergmann^{1

2

3}

Affiliations

¹ Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
² Swiss Institute of Bioinformatics, Lausanne, Switzerland.
³ Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.

Abstract

Summary: 'PascalX' is a Python library providing fast and accurate tools for mapping SNP-wise GWAS summary statistics. Specifically, it allows for scoring genes and annotated gene sets for enrichment signals based on data from, both, single GWAS and pairs of GWAS. The gene scores take into account the correlation pattern between SNPs. They are based on the cumulative density function of a linear combination of χ2 distributed random variables, which can be calculated either approximately or exactly to high precision. Acceleration via multithreading and GPU is supported. The code of PascalX is fully open source and well suited as a base for method development in the GWAS enrichment test context.

Availability and implementation: The source code is available at https://github.com/BergmannLab/PascalX and archived under doi://10.5281/zenodo.4429922. A user manual with usage examples is available at https://bergmannlab.github.io/PascalX/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Library
Genome-Wide Association Study*
Libraries*
Polymorphism, Single Nucleotide
Software