mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies.
mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies.
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mrMLM v4.0.2：用于多位点全基因组关联研究的 R 平台
DOI：
10.1016/j.gpb.2020.06.006
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发表时间：
2020-08
期刊：
影响因子：
--
通讯作者：
Zhang YM
中科院分区：
文献类型：
--
作者：
Zhang YW;Tamba CL;Wen YJ;Li P;Ren WL;Ni YL;Gao J;Zhang YM
以往的研究报告指出，单位点全基因组关联研究（GWAS）中遗漏了一些重要的位点，特别是田间试验中存在较大的表型误差。为了解决这个问题，多位点GWAS方法已被推荐。然而，只有少数几个软件包的多位点GWAS。因此，我们开发了一个R软件，名为mrMLM v4.0.2。该软件集成了本实验室开发的mrMLM、FASTMrMLM、FASTMrEMMA、pLARmEB、pKWmEB和ISIS EM-BLASSO方法。mrMLM v4.0.2中有四个组件，包括数据集输入、参数设置、软件运行和结果输出。data.table中的fread函数用于快速读取数据集，特别是大数据集，doParallel包用于使用多个CPU进行并行计算。此外，基于Shiny的图形用户界面软件mrMLM.GUI v4.0.2也可以使用。为了确认上述程序的正确性，使用mrMLM v4.0.2中的所有方法和三种广泛使用的方法来分析真实的和模拟数据集。结果证实了mrMLM v4.0.2的性能上级目前可用的其他方法。假阳性率得到有效控制，尽管显著性阈值不太严格。mrMLM v4.0.2可在BioCode（https：//bigd.big.ac.cn/biocode/tools/BT007077）或R（https：//cran.r-project.org/web/packages/mrMLM.GUI/index.html）上作为开源软件公开获取。
Previous studies have reported that some important loci are missed in single-locus genome-wide association studies (GWAS), especially because of the large phenotypic error in field experiments. To solve this issue, multi-locus GWAS methods have been recommended. However, only a few software packages for multi-locus GWAS are available. Therefore, we developed an R software named mrMLM v4.0.2. This software integrates mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, and ISIS EM-BLASSO methods developed by our lab. There are four components in mrMLM v4.0.2, including dataset input, parameter setting, software running, and result output. The fread function in data.table is used to quickly read datasets, especially big datasets, and the doParallel package is used to conduct parallel computation using multiple CPUs. In addition, the graphical user interface software mrMLM.GUI v4.0.2, built upon Shiny, is also available. To confirm the correctness of the aforementioned programs, all the methods in mrMLM v4.0.2 and three widely-used methods were used to analyze real and simulated datasets. The results confirm the superior performance of mrMLM v4.0.2 to other methods currently available. False positive rates are effectively controlled, albeit with a less stringent significance threshold. mrMLM v4.0.2 is publicly available at BioCode (https://bigd.big.ac.cn/biocode/tools/BT007077) or R (https://cran.r-project.org/web/packages/mrMLM.GUI/index.html) as an open-source software.
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影响因子：
4.5
作者：
Liu X;Huang M;Fan B;Buckler ES;Zhang Z
通讯作者：
Zhang Z
pLARmEB：最小角回归与经验贝叶斯的集成，用于多位点全基因组关联研究
影响因子：
3.8
作者：
Zhang J;Feng JY;Ni YL;Wen YJ;Niu Y;Tamba CL;Yue C;Song Q;Zhang YM
通讯作者：
Zhang YM
影响因子：
3.3
作者：
Raj A;Stephens M;Pritchard JK
通讯作者：
Pritchard JK
影响因子：
30.8
作者：
Loh, Po-Ru;Tucker, George;Bulik-Sullivan, Brendan K.;Vilhjalmsson, Bjarni J.;Finucane, Hilary K.;Salem, Rany M.;Chasman, Daniel I.;Ridker, Paul M.;Neale, Benjamin M.;Berger, Bonnie;Patterson, Nick;Price, Alkes L.
通讯作者：
Price, Alkes L.
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.