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

Description Usage Arguments Details Author(s) References Examples

Description

Conduct multi-locus genome-wide association study under the framework of 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 model, their effects are estimated by empirical Bayes and true QTNs are identified by likelihood ratio test.

Usage

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mrMLM(fileGen,filePhe,fileKin,filePS,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.

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: 3.1
Date: 2018-8-4
Depends: MASS,data.table,doParallel,foreach
Imports: methods,openxlsx,stringr,qqman,ggplot2,lars,ncvreg,coin
License: GPL version 2 or newer
LazyLoad: yes

Author(s)

Zhang Ya-Wen, Li Pei, Ren Wen-Long, Ni Yuan-Li, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[email protected]>

References

Methodological implementation of mixed linear models in multi-locus genome-wide association studies. Yang-Jun Wen,Hanwen Zhang,Yuan-Li Ni,Bo Huang,Jin Zhang,Jian-Ying Feng,Shi-Bo Wang,Jim M.Dunwell,Yuan-Ming Zhang,Rongling Wu.

Examples

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G1=data(Gen)
P1=data(Phe)
mrMLM(fileGen=Gen,filePhe=Phe,fileKin=NULL,filePS=NULL,Genformat="Num",
method=c("ISIS EM-BLASSO"),Likelihood="REML",trait=1:1,SearchRadius=20,
CriLOD=3,SelectVariable=50,Bootstrap=FALSE,
DrawPlot=FALSE,Plotformat="jpeg",Resolution="Low",dir=tempdir())

mrMLM documentation built on May 2, 2019, 8:17 a.m.