mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies

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...

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Autores principales: Zhang, Ya-Wen, Tamba, Cox Lwaka, Wen, Yang-Jun, Li, Pei, Ren, Wen-Long, Ni, Yuan-Li, Gao, Jun, Zhang, Yuan-Ming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8242264/
https://www.ncbi.nlm.nih.gov/pubmed/33346083
http://dx.doi.org/10.1016/j.gpb.2020.06.006
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author Zhang, Ya-Wen
Tamba, Cox Lwaka
Wen, Yang-Jun
Li, Pei
Ren, Wen-Long
Ni, Yuan-Li
Gao, Jun
Zhang, Yuan-Ming
author_facet Zhang, Ya-Wen
Tamba, Cox Lwaka
Wen, Yang-Jun
Li, Pei
Ren, Wen-Long
Ni, Yuan-Li
Gao, Jun
Zhang, Yuan-Ming
author_sort Zhang, Ya-Wen
collection PubMed
description 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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spelling pubmed-82422642021-07-02 mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies Zhang, Ya-Wen Tamba, Cox Lwaka Wen, Yang-Jun Li, Pei Ren, Wen-Long Ni, Yuan-Li Gao, Jun Zhang, Yuan-Ming Genomics Proteomics Bioinformatics Application Note 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. Elsevier 2020-08 2020-12-18 /pmc/articles/PMC8242264/ /pubmed/33346083 http://dx.doi.org/10.1016/j.gpb.2020.06.006 Text en © 2020 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Application Note
Zhang, Ya-Wen
Tamba, Cox Lwaka
Wen, Yang-Jun
Li, Pei
Ren, Wen-Long
Ni, Yuan-Li
Gao, Jun
Zhang, Yuan-Ming
mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies
title mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies
title_full mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies
title_fullStr mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies
title_full_unstemmed mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies
title_short mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies
title_sort mrmlm v4.0.2: an r platform for multi-locus genome-wide association studies
topic Application Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8242264/
https://www.ncbi.nlm.nih.gov/pubmed/33346083
http://dx.doi.org/10.1016/j.gpb.2020.06.006
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