WenS: The second step of Wen method

In QTL.gCIMapping.GUI: QTL Genome-Wide Composite Interval Mapping with Graphical User Interface

Description

An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2

Usage

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

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.

Author(s)

Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, Zhang Yuan-Ming
Maintainer: Yuanming Zhang<[e-mail]>

Examples

## Not run: 
data(genf2)
data(phef2)
data(mapf2)
WEN1re<-WenF(pheRaw=phef2,genRaw=genf2,mapRaw1=mapf2,
yygg1=NULL,cov_en=NULL,WalkSpeed=1,CriLOD=2.5,dir=tempdir())
###
ws<-WenS(flag=1,CriLOD=2.5,NUM=1,pheRaw=phef2,
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())

## End(Not run)

QTL.gCIMapping.GUI documentation built on Oct. 23, 2020, 8:13 p.m.