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

Llinares-López, Felipe; Papaxanthos, Laetitia; Roqueiro, Damian; Bodenham, Dean; Borgwardt, Karsten

doi:10.1093/bioinformatics/bty1020

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

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https://github.com/BorgwardtLab/CAsMap
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Llinares-López, F., Papaxanthos, L., Roqueiro, D., Bodenham, D., & Borgwardt, K. (2019). CASMAP: detection of statistically significant combinations of SNPs in association mapping. Bioinformatics, 35(15), 2680-2682. doi:10.1093/bioinformatics/bty1020.

Cite as: https://hdl.handle.net/21.11116/0000-000C-F0EC-B

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.