FASTmrEMMA | R Documentation |
FAST multi-locus random-SNP-effect EMMA
FASTmrEMMA(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,Likelihood,CLO)
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. |
Zhang Ya-Wen, Wang Jing-Tian, Li Pei, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
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)
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