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.

以前的研究报告说，在单基因座全基因组关联研究(GWAS)中遗漏了一些重要的基因座，特别是因为田间实验中存在较大的表型错误。为了解决这个问题，已经推荐了多位点 GWAS 方法。但是，只有少数用于多位点 GWAS 的软件包可用。因此，我们开发了一款名为mrMLM v4.0.2的R软件。该软件集成了我们实验室开发的mrMLM、FASTmrMLM、FASTmrEMMA、pLARmEB、pKWmEB和ISIS EM-BLASSO方法。mrMLM v4.0.2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。该FREADdata.table 中的函数用于快速读取数据集，尤其是大数据集，doParallel 包用于使用多个 CPU 进行并行计算。此外，还提供基于 Shiny 的图形用户界面软件 mrMLM.GUI v4.0.2。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和模拟数据集。结果证实了 mrMLM v4.0.2 相对于目前可用的其他方法的优越性能。尽管显着性阈值不那么严格，但假阳性率得到了有效控制。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) 作为开源软件。