pLARmEB {mrMLM}

To perform GWAS with pLARmEB method

Description

polygene-background-control-based least angle regression plus Empirical Bayes

Usage

pLARmEB(gen,phe,outATCG,genRaw,kk,psmatrix,CriLOD,lars1,Genformat,Bootstrap,CLO)

Arguments

gen

genotype matrix.

phe

phenotype matrix.

outATCG

genotype for code 1.

genRaw

raw genotype.

kk

kinship matrix.

psmatrix

population structure matrix.

CriLOD

Critical LOD score for significant QTN.

lars1

No. of potentially associated variables selected by LARS.

Genformat

Format for genotypic codes.

Bootstrap

Bootstrap=FALSE indicates the analysis of only real dataset, Bootstrap=TRUE indicates the analysis of both real dataset and four resampling datasets.

CLO

number of CPU.

Author(s)

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

Examples

G1=data(Gen)
P1=data(Phe)
Readraw=ReadData(fileGen=Gen,filePhe=Phe,fileKin=NULL,filePS =NULL,
Genformat=1)
InputData=inputData(readraw=Readraw,Genformat=1,method="pLARmEB",trait=1)
result=pLARmEB(InputData$doMR$gen,InputData$doMR$phe,InputData$doMR$outATCG,
InputData$doMR$genRaw,InputData$doMR$kk,InputData$doMR$psmatrix,
CriLOD=3,lars1=20,Genformat=1,Bootstrap=FALSE,CLO=1)