ZhouMethod_single_env: The second step of Zhou method for single environment

In QTL.gCIMapping: QTL Genome-Wide Composite Interval Mapping

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)

QTL.gCIMapping documentation built on March 18, 2022, 5:54 p.m.