mrMLM (version 5.0.1)

FASTmrEMMA: 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.

Examples

# NOT RUN {
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)   
# }