ZhouMethod | R Documentation |
The second step of Zhou method for multiple environments
ZhouMethod( Model = NULL, pheRaw = NULL, genRaw = NULL, mapRaw = NULL, CriLOD = NULL, NUM = NULL, EnvNum = NULL, yygg = NULL, genoname = NULL, Ax0 = NULL, Hx0 = NULL, Bx0 = NULL, Ax = NULL, Hx = NULL, Bx = NULL, dir = NULL, CriDis = NULL, CLO = NULL )
Model |
Random or fixed model. |
pheRaw |
phenotype matrix. |
genRaw |
genotype matrix. |
mapRaw |
linkage map matrix. |
CriLOD |
Critical LOD scores for significant QTL. |
NUM |
The serial number of the trait to be analyzed. |
EnvNum |
The number of environments for each trait is a vector. |
yygg |
covariate matrix. |
genoname |
linkage map matrix with pseudo markers inserted. |
Ax0 |
AA genotype matrix. |
Hx0 |
Aa genotype matrix. |
Bx0 |
aa genotype matrix. |
Ax |
AA genotype matrix with pseudo markers inserted. |
Hx |
Aa genotype matrix with pseudo markers inserted. |
Bx |
aa genotype matrix with pseudo markers inserted. |
dir |
file storage path. |
CriDis |
The distance of optimization. |
CLO |
Number of CPUs. |
a list
data(F2data) readraw<-Readdata(file=F2data,fileFormat="GCIM", method="GCIM-QEI",filecov=NULL, MCIMmap=NULL,MultiEnv=TRUE) DoResult<-Dodata(fileFormat="GCIM", Population="F2",method="GCIM-QEI", Model="Random",readraw,MultiEnv=TRUE) ZhouMatrices<-ZhouF(pheRaw=DoResult$pheRaw, genRaw=DoResult$genRaw,mapRaw1=DoResult$mapRaw1, WalkSpeed=1,CriLOD=3,dir=tempdir()) OutputZhou<-ZhouMethod(Model="Random", pheRaw=DoResult$pheRaw,genRaw=DoResult$genRaw, mapRaw=ZhouMatrices$mapRaw,CriLOD=3,NUM=1, EnvNum=DoResult$EnvNum,yygg=DoResult$yygg1, genoname=ZhouMatrices$genoname, Ax0=ZhouMatrices$Ax0,Hx0=ZhouMatrices$Hx0, Bx0=ZhouMatrices$Bx0,Ax=ZhouMatrices$Ax, Hx=ZhouMatrices$Hx,Bx=ZhouMatrices$Bx, dir=tempdir(),CriDis=5,CLO=2)
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