FASTmrEMMA: To perform GWAS with FASTmrEMMA method
In mrMLM: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for GWAS

FASTmrEMMA

R Documentation

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<soyzhang@mail.hzau.edu.cn>

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)

mrMLM documentation built on March 27, 2022, 9:05 a.m.