CASMAP: Detection of statistically significant combinations of SNPs in association mapping

Abstract

Summary: Combinatorial association mapping aims to assess the statistical association of higher-order interactions of genetic markers with a phenotype of interest. This article presents combinatorial association mapping (CASMAP), a software package that leverages recent advances in significant pattern mining to overcome the statistical and computational challenges that have hindered combinatorial association mapping. CASMAP can be used to perform region-based association studies and to detect higher-order epistatic interactions of genetic variants. Most importantly, unlike other existing significant pattern mining-based tools, CASMAP allows for the correction of categorical covariates such as age or gender, making it suitable for genome-wide association studies. Availability and implementation: The R and Python packages can be downloaded from our GitHub repository http://github.com/BorgwardtLab/CASMAP. The R package is also available on CRAN. Supplementary information: Supplementary data are available at Bioinformatics online.