ZhouMethod_single_env {QTL.gCIMapping}

The second step of Zhou method for single environment

Description

The second step of Zhou method for single environment

Usage

ZhouMethod_single_env(
  Model = NULL,
  pheRaw = NULL,
  genRaw = NULL,
  mapRaw = NULL,
  CriLOD = NULL,
  NUM = NULL,
  yygg = NULL,
  genoname = NULL,
  Ax0 = NULL,
  Hx0 = NULL,
  Bx0 = NULL,
  Ax = NULL,
  Hx = NULL,
  Bx = NULL,
  dir = NULL,
  CriDis = NULL,
  CLO = NULL
)

Arguments

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.

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.

Value

a list

Examples

data(F2data)
readraw<-Readdata(file=F2data,fileFormat="GCIM",
method="GCIM-QEI",filecov=NULL,
MCIMmap=NULL,MultiEnv=FALSE)
DoResult<-Dodata(fileFormat="GCIM",Population="F2",
method="GCIM-QEI",Model="Random",
readraw,MultiEnv=FALSE)
ZhouMatrices<-ZhouF(pheRaw=DoResult$pheRaw,
genRaw=DoResult$genRaw,mapRaw1=DoResult$mapRaw1,
WalkSpeed=1,CriLOD=3,dir=tempdir())
OutputZhou<-ZhouMethod_single_env(Model="Random",
pheRaw=DoResult$pheRaw,genRaw=DoResult$genRaw,
mapRaw=ZhouMatrices$mapRaw,CriLOD=3,NUM=1,
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)