QTL Genome-Wide Composite Interval Mapping with Graphical User Interface

Description

Conduct multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect mixed linear model. First, each position on the genome is detected in order to construct a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid or by adaptive lasso in F2, and true QTL are identified by likelihood radio test.

Usage

QTL.gCIMapping.GUI()

Details

Author(s)

Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

References

An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2.Wen Yang-Jun, Zhang Ya-Wen, Zhang Jin, Feng Jian-Ying, Jim M. Dunwell, Zhang Yuan-Ming*

Examples

## Not run: QTL.gCIMapping.GUI()

To perform QTL mapping with wang method

Description

Genome-wide Composite Interval Mapping

Usage

WangF(pheRaw,genRaw,mapRaw1,yygg1,flagRIL,cov_en,Population,WalkSpeed,CriLOD)

Arguments

Author(s)

Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

Examples

## Not run: 
data(gen)
data(phe)
data(map)
wf<-WangF(pheRaw=phe,genRaw=gen,mapRaw1=map,yygg1=NULL,
flagRIL=0,cov_en=NULL,Population="DH",WalkSpeed=1,CriLOD=2.5)

## End(Not run)

The second step of wang method

Description

Genome-wide Composite Interval Mapping

Usage

WangS(flag,CriLOD,NUM,pheRaw,chrRaw_name,yygg,mx,phe,chr_name,gen,
mapname,CLO)

Arguments

Author(s)

Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

Examples

## Not run: 
data(gen)
data(phe)
data(map)
W1re<-WangF(pheRaw=phe,genRaw=gen,mapRaw1=map,yygg1=NULL,
flagRIL=0,cov_en=NULL,Population="DH",WalkSpeed=1,CriLOD=2.5)
###
ws<-WangS(flag=1,CriLOD=2.5,NUM=1,pheRaw=phe,
chrRaw_name=W1re$chrRaw_name,yygg=W1re$yygg,mx=W1re$mx,
phe=W1re$phe,chr_name=W1re$chr_name,gen=W1re$gen,
mapname=W1re$mapname,CLO=1)

## End(Not run)

To perform QTL mapping with Wen method

Description

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

Usage

WenF(pheRaw,genRaw,mapRaw1,yygg1,cov_en,WalkSpeed,CriLOD,dir)

Arguments

Author(s)

Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

Examples

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

## End(Not run)

The second step of Wen method

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

Author(s)

Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

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)

genotype example data

Description

GCIM format of DH genotype dataset.

Usage

  data(gen)

Details

Dataset input of file for WangF function.

Author(s)

Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

genotype example data

Description

GCIM format of F2 genotype dataset.

Usage

  data(genf2)

Details

Dataset input of file for WenF function.

Author(s)

Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

map example data

Description

GCIM format of DH map dataset.

Usage

  data(map)

Details

Dataset input of file for WangF function.

Author(s)

Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

map example data

Description

GCIM format of F2 map dataset.

Usage

  data(mapf2)

Details

Dataset input of file for WenF function.

Author(s)

Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

To insert marker in genotype.

Description

a method that can insert marker in genotype.

Usage

markerinsert(mp,geno,map,cl,gg1,gg2,gg0,flagRIL)

Arguments

Author(s)

Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

Examples

## Not run: 
mp<-matrix(c(197.9196,198.7536,199.5876,200.4216,201.2453,
202.0691,202.8928,203.7521,204.6113,205.4706,206.3298,207.1891,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,3,3,3,3,3,3,
1,1,1,2,2,2,3,3,3,3,3,3,1,2,3,4,5,6,7,8,9,10,11,12),12,5)
map<-matrix(c(1,1,1,1,197.9196,200.4216,202.8928,207.1891),4,2)
geno<-matrix(c(1,99,99,99),1,4)
mark_insert<-QTL.gCIMapping::markerinsert(mp,geno,map,cl=1,gg1=1,gg2=-1,
gg0=99,flagRIL=1)

## End(Not run)

phenotype example data

Description

GCIM format of DH phenotype dataset.

Usage

  data(phe)

Details

Dataset input of file for WangF function.

Author(s)

Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>

phenotype example data

Description

GCIM format of F2 phenotype dataset.

Usage

  data(phef2)

Details

Dataset input of file for WenF function.

Author(s)

Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>