FASTmrEMMA {mrMLM}

To perform GWAS with FASTmrEMMA method

Description

FAST multi-locus random-SNP-effect EMMA

Usage

FASTmrEMMA(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,Likelihood,CLO)

Arguments

gen

genotype matrix.

phe

phenotype matrix.

outATCG

genotype for code 1.

genRaw

raw genotype.

kk

kinship matrix.

psmatrix

population structure matrix.

svpal

Critical P-value for selecting variable.

svmlod

Critical LOD score for significant QTN.

Genformat

Format for genotypic codes.

Likelihood

restricted maximum likelihood (REML) and maximum likelihood (ML).

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="FASTmrEMMA",trait=1)
result=FASTmrEMMA(InputData$doFME$gen,InputData$doFME$phe,
InputData$doFME$outATCG,InputData$doFME$genRaw,
InputData$doFME$kk,InputData$doFME$psmatrix,0.005,
svmlod=3,Genformat=1,Likelihood="REML",CLO=1)