MCPerm: A Monte Carlo Permutation Method for Accurately Correcting the Multiple Testing in a Meta-Analysis of Genetic Association Studies
文献类型：期刊论文
| 作者 | Jiang, Yongshuai1; Zhang, Lanying1; Kong, Fanwu2; Zhang, Mingming1; Lv, Hongchao1; Liu, Guiyou3; Liao, Mingzhi4; Feng, Rennan5; Li, Jin1; Zhang, Ruijie1 |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2014-02-21 |
| 卷号 | 9期号:2 |
| 英文摘要 | Traditional permutation (TradPerm) tests are usually considered the gold standard for multiple testing corrections. However, they can be difficult to complete for the meta-analyses of genetic association studies based on multiple single nucleotide polymorphism loci as they depend on individual-level genotype and phenotype data to perform random shuffles, which are not easy to obtain. Most meta-analyses have therefore been performed using summary statistics from previously published studies. To carry out a permutation using only genotype counts without changing the size of the TradPerm P-value, we developed a Monte Carlo permutation (MCPerm) method. First, for each study included in the meta-analysis, we used a two-step hypergeometric distribution to generate a random number of genotypes in cases and controls. We then carried out a meta-analysis using these random genotype data. Finally, we obtained the corrected permutation P-value of the meta-analysis by repeating the entire process N times. We used five real datasets and five simulation datasets to evaluate the MCPerm method and our results showed the following: (1) MCPerm requires only the summary statistics of the genotype, without the need for individual-level data; (2) Genotype counts generated by our two-step hypergeometric distributions had the same distributions as genotype counts generated by shuffling; (3) MCPerm had almost exactly the same permutation P-values as TradPerm (r = 0.999; P < 2.2e-16); (4) The calculation speed of MCPerm is much faster than that of TradPerm. In summary, MCPerm appears to be a viable alternative to TradPerm, and we have developed it as a freely available R package at CRAN: http://cran.r-project.org/web/packages/MCPerm/index.html. |
| WOS标题词 | Science & Technology |
| 类目[WOS] | Multidisciplinary Sciences |
| 研究领域[WOS] | Science & Technology - Other Topics |
| 关键词[WOS] | GENOME-WIDE ASSOCIATION ; SYSTEMATIC METAANALYSES ; HETEROGENEITY ; SCHIZOPHRENIA ; VARIANCE ; DATABASE ; REVIEWS |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000331717900062 |
| 源URL | [http://124.16.173.210/handle/834782/1396]  |
| 专题 | 天津工业生物技术研究所_基因组分析实验室 陈祖耕_期刊论文 |
| 作者单位 | 1.Harbin Med Univ, Coll Bioinformat Sci & Technol, Harbin, Peoples R China 2.Harbin Med Univ, Affiliated Hosp 2, Dept Nephrol, Harbin, Peoples R China 3.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Genome Anal Lab, Tianjin, Peoples R China 4.Northwest A&F Univ, Coll Life Sci, Yangling, Shaanxi, Peoples R China 5.Harbin Med Univ, Sch Publ Hlth, Dept Nutr & Food Hyg, Harbin, Peoples R China |
| 推荐引用方式 GB/T 7714 | Jiang, Yongshuai,Zhang, Lanying,Kong, Fanwu,et al. MCPerm: A Monte Carlo Permutation Method for Accurately Correcting the Multiple Testing in a Meta-Analysis of Genetic Association Studies[J]. PLOS ONE,2014,9(2). |
| APA | Jiang, Yongshuai.,Zhang, Lanying.,Kong, Fanwu.,Zhang, Mingming.,Lv, Hongchao.,...&Zhang, Ruijie.(2014).MCPerm: A Monte Carlo Permutation Method for Accurately Correcting the Multiple Testing in a Meta-Analysis of Genetic Association Studies.PLOS ONE,9(2). |
| MLA | Jiang, Yongshuai,et al."MCPerm: A Monte Carlo Permutation Method for Accurately Correcting the Multiple Testing in a Meta-Analysis of Genetic Association Studies".PLOS ONE 9.2(2014). |
入库方式： OAI收割
来源：天津工业生物技术研究所
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