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

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

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

Description

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 true 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>).

Usage

mrMLM(fileGen,filePhe,fileKin,filePS,PopStrType,fileCov,Genformat,
method,Likelihood,trait,SearchRadius,CriLOD,SelectVariable,Bootstrap,
DrawPlot,Plotformat,dir,PC,RAM)

Arguments

fileGen	File path and name in your computer of Genotype, i.e.,"D:/Users/Genotype_num.csv".
filePhe	File path and name in your computer of Phenotype, i.e.,"D:/Users/Phenotype.csv".
fileKin	File path and name in your computer of Kinship, i.e.,"D:/Users/Kinship.csv".
filePS	File path and name in your computer of Population Structure,i.e.,"D:/Users/PopStr.csv".
PopStrType	The type of population structure,i.e.,Q (Q matrix), PCA (principal components), EvolPopStr (evolutionary population structure).
fileCov	File path and name in your computer of covariate, i.e.,"D:/Users/Covariate.csv".
Genformat	Format for genotypic codes, Num (number), Cha (character) and Hmp (Hapmap).
method	Six multi-locus GWAS methods. Users may select one to six methods, including mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB and ISIS EM-BLASSO.
Likelihood	This parameter is only for FASTmrEMMA, including REML(restricted maximum likelihood) and ML(maximum likelihood).
trait	Traits analyzed from number 1 to number 2,i.e.,1:2.
SearchRadius	This parameter is only for mrMLM and FASTmrMLM, indicating Search Radius in search of potentially associated QTN,the default is 20.
CriLOD	Critical LOD score for significant QTN.
SelectVariable	This parameter is only for pLARmEB. SelectVariable=50 indicates that 50 potentially associated variables are selected from each chromosome. Users may change this number in real data analysis in order to obtain the best results as final results,the default is 50.
Bootstrap	This parameter is only for pLARmEB, including FASLE and TRUE, Bootstrap=FALSE indicates the analysis of only real dataset, Bootstrap=TRUE indicates the analysis of both real dataset and four resampling datasets,the default is FALSE.
DrawPlot	This parameter is for all the six methods, including FALSE and TRUE, DrawPlot=FALSE indicates no figure output, DrawPlot=TRUE indicates the output of the Manhattan, QQ figures,the default is TRUE.
Plotformat	This parameter is for all the figure files, including *.jpeg, *.png, *.tiff and *.pdf,the default is "tiff".
dir	This parameter is for the save path,i.e.,"D:/Users"
PC	This parameter is used to specify whether only small RAM device is available to run the mrMLM program, such as desktop or laptop. The default value is PC=FALSE. PC=TRUE indicates running the program on low RAM desktop or laptop.
RAM	This parameter is the RAM of your desktop or laptop. The default value is RAM=4. RAM=4 indicates the RAM of your device is 4G.

Details

Package:	mrMLM
Type:	Package
Version:	5.0.1
Date:	2022-3-27
Depends:	lars
Imports:	methods,foreach,ncvreg,coin,sampling,data.table,doParallel,BEDMatrix
License:	GPL version 2 or newer
LazyLoad:	yes

Note

Once the running of the software mrMLM v5.0.1 is ended, the "results" files should appear on the Directory, which was set up by users before running the software. The results for each trait include "*_intermediate result.csv", "*_Final result.csv", Manhattan plot, and QQ plot. If only pLARmEB and ISIS EM-BLASSO methods are selected, there will be no intermediate results and figures output. Users can decompress the mrMLM package and find the User Manual file (name: Instruction.pdf) in the folder of ".../mrMLM/inst".

Author(s)

Zhang Ya-Wen, Wang Jing-Tian, Li Pei, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[e-mail]>

References

1. Zhang YM, Mao Y, Xie C, Smith H, Luo L, Xu S. Genetics 2005,169:2267-2275. 2. Wang SB, Feng JY, Ren WL, Huang B, Zhou L, Wen YJ, Zhang J, Dunwell JM, Xu S, Zhang YM. Sci Rep 2016,6:19444. 3. Tamba CL, Ni YL, Zhang YM. PLoS Comput Biol 2017,13(1):e1005357. 4. Zhang J, Feng JY, Ni YL, Wen YJ, Niu Y, Tamba CL, Yue C, Song Q, Zhang YM. Heredity 2018,118(6):517-524. 5. Ren WL, Wen YJ, Dunwell JM, Zhang YM. Heredity 2018,120(3): 208-218. 6. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R. Brief Bioinform 2018,19(4): 700-712. 7. Tamba CL, Zhang YM. bioRxiv,preprint first posted online Jun. 7, 2018, doi:https://doi.org/10.1101/341784. 8. Zhang YW, Tamba CL, Wen YJ, Li P, Ren WL, Ni YL, Gao J, Zhang YM. Genomics, Proteomics & Bioinformatics 2020, 18: 481-487. 9.Li M, Zhang YW, Zhang ZC, Xiang Y, Liu MH, Zhou YH, Zuo JF, Zhang HQ, Chen Y, Zhang YM. A compressed variance component mixed model for detecting QTNs, and QTN-by-environment and QTN-by-QTN interactions in genome-wide association studies. Molecular Plant 2022, online, S1674-2052(22)00060-0. doi: 10.1016/j.molp.2022.02.012.

Examples

Ge1=data(Genotype)
Ph1=data(Phenotype)
mrMLM(fileGen=Genotype,filePhe=Phenotype,Genformat="Num",
method=c("FASTmrMLM"),trait=1,CriLOD=3,DrawPlot=FALSE,
dir=tempdir(),PC=FALSE,RAM=4)

mrMLM documentation built on March 27, 2022, 9:05 a.m.