WenS: The second step of Wen method

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

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

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())

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