PHESANT

PHESANT performs comprehensive phenome scans that test associations between a specified trait and continuous, integer, and categorical variables in the UK Biobank to support phenome-wide association studies and Mendelian randomization analyses.

Key Features:

• Comprehensive phenotype analysis: Tests associations between a specified trait and all continuous, integer, and categorical variables in the UK Biobank and can focus on a user-defined subset of phenotypes.
• Rule-based algorithm: Employs a rule-based algorithm that determines the appropriate statistical method for testing each phenotype association.
• Implementation in R: Implemented in the R programming language for data manipulation and statistical analysis.
• Visualization and data conversion: Integrates JavaScript D3.js for visualization of phenome scan results and includes Java code to convert results into JSON.

Scientific Applications:

• Phenome-wide association studies (pheWAS): Enables systematic scanning of UK Biobank phenotypes to identify trait associations.
• Mendelian randomization analyses: Supports Mendelian randomization to investigate potential causal relationships between traits using biobank data.
• Genetic epidemiology and complex trait investigation: Facilitates investigations into complex trait associations and genetic epidemiology within large-scale biobank datasets.

Methodology:

Implemented in R, PHESANT uses a rule-based algorithm to select statistical tests per phenotype, integrates JavaScript D3.js for visualization, and includes Java code to convert results into JSON.