Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs.
Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs.
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DOI：
10.1093/bioinformatics/btn616
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发表时间：
2009-01-15
期刊：
影响因子：
--
通讯作者：
Hoque MA
中科院分区：
文献类型：
--
作者：
Kitamura N;Akazawa K;Miyashita A;Kuwano R;Toyabe S;Nakamura J;Nakamura N;Sato T;Hoque MA
动机：在有效识别疾病易感基因的多阶段设计中，两阶段关联研究是最常用的方法。最近，一些SNP研究已经利用两个以上的阶段来检测疾病基因。然而，几乎没有可用的程序来计算任意n阶段设计的统计功率和正预测值(PPV)。结果：我们使用R语言开发了多阶段病例对照关联研究的程序。在我们的程序中，输入参数包括样本和候选基因座的数量、全基因组假阳性率以及在第k阶段(k=1，…)选择的样本和基因座的比例，n)。该程序在任意n阶段设计中输出统计功率、PPV和打字次数。在计划全基因组关联研究时，这些程序可以为各种条件下的先前模拟做出贡献。可获得性：R计划可供学术用户免费使用，并可从http://www.med.niigata-u.ac.jp/eng/resources/informatics/gwa.html下载。
Motivation: A two-stage association study is the most commonly used method among multistage designs to efficiently identify disease susceptibility genes. Recently, some SNP studies have utilized more than two stages to detect disease genes. However, there are few available programs for calculating statistical powers and positive predictive values (PPVs) of arbitrary n-stage designs. Results: We developed programs for a multistage case–control association study using R language. In our programs, input parameters include numbers of samples and candidate loci, genome-wide false positive rate and proportions of samples and loci to be selected at the k-th stage (k=1,…, n). The programs output statistical powers, PPVs and numbers of typings in arbitrary n-stage designs. The programs can contribute to prior simulations under various conditions in planning a genome-wide association study. Availability: The R programs are freely available for academic users and can be downloaded from http://www.med.niigata-u.ac.jp/eng/resources/informatics/gwa.html Contact: nktmr@m12.alpha-net.ne.jp Supplementary information: Supplementary data are available at Bioinformatics online.
影响因子：
1.9
作者：
Satagopan, JM;Verbel, DA;Begg, CB
通讯作者：
Begg, CB
影响因子：
30.8
作者：
Skol, AD;Scott, LJ;Boehnke, M
通讯作者：
Boehnke, M
影响因子：
2.1
作者：
Prentice, Ross L.;Qi, Lihong
通讯作者：
Qi, Lihong