CASMAP: detection of statistically significant combinations of SNPs in association mapping
CASMAP: detection of statistically significant combinations of SNPs in association mapping
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DOI：
10.1093/bioinformatics/bty1020
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发表时间：
2019-08-01
期刊：
影响因子：
5.8
通讯作者：
Borgwardt, Karsten
中科院分区：
文献类型：
--
作者：
Llinares-Lopez, Felipe;Papaxanthos, Laetitia;Borgwardt, Karsten
组合关联作图旨在评估遗传标记与感兴趣的表型的高阶相互作用的统计关联。本文介绍了组合关联映射（CASMAP），一个软件包，利用最新进展的重要模式挖掘，以克服统计和计算的挑战，阻碍了组合关联映射。CASMAP可用于进行基于区域的关联研究，并检测遗传变异的高阶上位相互作用。最重要的是，与其他现有的基于显著模式挖掘的工具不同，CASMAP允许校正分类协变量，如年龄或性别，使其适用于全基因组关联研究。可用性和实施R和Python包可以从我们的GitHub存储库http://github.com/BorgwardtLab/CASMAP下载。R软件包也可以在CRAN上获得。补充信息补充数据可以在Bioinformatics在线获得。
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 informationSupplementary data are available at Bioinformatics online.