mrMLM {mrMLM} | R Documentation |
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 ture QTL.
mrMLM(fileGen,filePhe,fileKin,filePS,PopStrType,fileCov,Genformat, method,Likelihood,trait,SearchRadius,CriLOD,SelectVariable,Bootstrap, DrawPlot,Plotformat,Resolution,dir)
fileGen |
File path and name in your computer of Genotype. |
filePhe |
File path and name in your computer of Phenotype. |
fileKin |
File path and name in your computer of Kinship. |
filePS |
File path and name in your computer of Population Structure. |
PopStrType |
The type of population structure. |
fileCov |
File path and name in your computer of covariate. |
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 restricted maximum likelihood (REML) and maximum likelihood (ML). |
trait |
Traits analyzed from number 1 to number 2. |
SearchRadius |
This parameter is only for mrMLM and FASTmrMLM, indicating Search Radius in search of potentially associated QTN. |
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. |
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. |
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 and LOD score against genome position figures. |
Plotformat |
This parameter is for all the figure files, including *.jpeg, *.png, *.tiff and *.pdf. |
Resolution |
This parameter is for all the figure files, including Low and High. |
dir |
This parameter is for the save path. |
Package: | mrMLM |
Type: | Package |
Version: | 4.0 |
Date: | 2019-10-21 |
Depends: | ggplt2,lars |
Imports: | methods,qqman,foreach,ncvreg,coin,sampling,data.table,doParallel |
License: | GPL version 2 or newer |
LazyLoad: | yes |
Zhang Ya-Wen, Li Pei, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
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, et al. 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, et al. 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, et al. 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, et al. Genomics, Proteomics & Bioinformatics, resubmission.
Ge1=data(Genotype) Ph1=data(Phenotype) mrMLM(fileGen=Genotype,filePhe=Phenotype,Genformat="Num",method=c("FASTmrMLM"), trait=1,CriLOD=3,dir=tempdir())