mrMLM {mrMLM}R Documentation

Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study

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 ture QTL.

Usage

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

Arguments

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.

Details

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

Author(s)

Zhang Ya-Wen, Li Pei, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>

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, 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.

Examples

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

[Package mrMLM version 4.0 Index]