mrMLM: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for GWAS

Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes, and all the nonzero effects were further identified by likelihood ratio test for significant QTL. The program may run on a desktop or laptop computers. If marker genotypes in association mapping population are almost homozygous, these methods in this software are very effective. If there are many heterozygous marker genotypes, the IIIVmrMLM software is recommended. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018, <doi:10.1093/bib/bbw145>), and Li M, Zhang YW, Zhang ZC, Xiang Y, Liu MH, Zhou YH, Zuo JF, Zhang HQ, Chen Y, Zhang YM (2022, <doi:10.1016/j.molp.2022.02.012>).

Version: 5.0.1
Depends: R (≥ 3.5.0), lars
Imports: Rcpp (≥ 0.12.14), methods, foreach, ncvreg, coin (≥ 1.1-0), sampling, data.table, doParallel, sbl, BEDMatrix
LinkingTo: Rcpp, RcppEigen
Published: 2022-03-27
Author: Ya-Wen Zhang [aut], Jing-Tian Wang [aut], Pei Li [aut], Yuan-Ming Zhang ORCID iD [aut, cre]
Maintainer: Yuan-Ming Zhang <soyzhang at mail.hzau.edu.cn>
Contact: Yuan-Ming Zhang <soyzhang@mail.hzau.edu.cn>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
CRAN checks: mrMLM results

Documentation:

Reference manual: mrMLM.pdf

Downloads:

Package source: mrMLM_5.0.1.tar.gz
Windows binaries: r-devel: mrMLM_5.0.1.zip, r-release: mrMLM_5.0.1.zip, r-oldrel: mrMLM_5.0.1.zip
macOS binaries: r-release (arm64): mrMLM_5.0.1.tgz, r-release (x86_64): mrMLM_5.0.1.tgz, r-oldrel: mrMLM_5.0.1.tgz
Old sources: mrMLM archive

Reverse dependencies:

Reverse imports: mrMLM.GUI

Linking:

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