QTL.gCIMapping (version 3.4)

WenS: The second step of Wen method

Description

The second step of Wen method

Usage

WenS(
  flag = NULL,
  CriLOD = NULL,
  NUM = NULL,
  pheRaw = NULL,
  Likelihood = NULL,
  SetSeed = NULL,
  flagrqtl = NULL,
  yygg = NULL,
  mx = NULL,
  phe = NULL,
  chr_name = NULL,
  v.map = NULL,
  gen.raw = NULL,
  a.gen.orig = NULL,
  d.gen.orig = NULL,
  n = NULL,
  names.insert2 = NULL,
  X.ad.tran.data = NULL,
  X.ad.t4 = NULL,
  dir = NULL
)

Arguments

flag

random or fix model.

CriLOD

LOD score.

NUM

the number of trait.

pheRaw

raw phenotype matrix.

Likelihood

likelihood function.

SetSeed

random seed set in which,the cross validation is needed.

flagrqtl

do CIM or not.

yygg

covariate matrix.

mx

raw genotype matrix.

phe

phenotype matrix.

chr_name

chromosome name.

v.map

linkage map matrix.

gen.raw

raw genotype matrix.

a.gen.orig

additive genotype matrix.

d.gen.orig

dominant genotype matrix.

n

number of individual.

names.insert2

linkage map after insert.

X.ad.tran.data

genotype matrix after insert.

X.ad.t4

genotype matrix.

dir

file storage path.

Value

a list

Examples

# NOT RUN {
data(F2data)
readraw<-Readdata(file=F2data,fileFormat="GCIM",
method="GCIM",filecov=NULL,MCIMmap=NULL,MultiEnv=FALSE)
DoResult<-Dodata(fileFormat="GCIM",Population="F2",
method="GCIM",Model="Random",readraw,MultiEnv=FALSE)
WEN1re<-WenF(pheRaw=DoResult$pheRaw,
genRaw=DoResult$genRaw,mapRaw1=DoResult$mapRaw1,
yygg1=DoResult$yygg1,cov_en=DoResult$cov_en,
WalkSpeed=1,CriLOD=2.5,dir=tempdir())
ws<-WenS(flag=DoResult$flag,CriLOD=2.5,NUM=1,
pheRaw=DoResult$pheRaw,Likelihood="REML",
SetSeed=11001,flagrqtl=FALSE,
yygg=WEN1re$yygg,mx=WEN1re$mx,phe=WEN1re$phe,
chr_name=WEN1re$chr_name,v.map=WEN1re$v.map,
gen.raw=WEN1re$gen.raw,
a.gen.orig=WEN1re$a.gen.orig,
d.gen.orig=WEN1re$d.gen.orig,n=WEN1re$n,
names.insert2=WEN1re$names.insert2,
X.ad.tran.data=WEN1re$X.ad.tran.data,
X.ad.t4=WEN1re$X.ad.t4,dir=tempdir())
# }