| Type: | Package |
| Title: | Segregation Analysis |
| Version: | 2.0.1 |
| Date: | 2022-3-28 |
| Maintainer: | Yuan-Ming Zhang <soyzhang@mail.hzau.edu.cn> |
| Contact: | Yuan-Ming Zhang <soyzhang@mail.hzau.edu.cn> |
| Description: | A few major genes and a series of polygene are responsive for each quantitative trait. Major genes are individually identified while polygene is collectively detected. This is mixed major genes plus polygene inheritance analysis or segregation analysis (SEA). In the SEA, phenotypes from a single or multiple bi-parental segregation populations along with their parents are used to fit all the possible models and the best model of the trait for population phenotypic distributions is viewed as the model of the trait. There are fourteen types of population combinations available. Zhang Yuan-Ming, Gai Jun-Yi, Yang Yong-Hua (2003, <doi:10.1017/S0016672303006141>). |
| Depends: | shiny,MASS,doParallel,foreach,methods |
| Imports: | KScorrect,utils,stats,grDevices,graphics,data.table |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| Packaged: | 2022-03-29 02:34:32 UTC; Administrator |
| Repository: | CRAN |
| Date/Publication: | 2022-03-30 07:30:12 UTC |
| Author: | Jing-Tian Wang [aut],
Ya-Wen Zhang [aut],
Yuan-Ming Zhang 
[aut, cre] |
Segregation Analysis
Description
A few major genes and a series of polygene are responsive for each quantitative trait. Major genes are individually identified while polygene is collectively detected. This is mixed major genes plus polygene inheritance analysis or segregation analysis (SEA). In the SEA, phenotypes from a single or multiple bi-parental segregation populations along with their parents are used to fit all the possible models and the best model for population phenotypic distributions is viewed as the model of the trait. There are fourteen types of population combinations available. Zhang Yuan-Ming, Gai Jun-Yi, Yang Yong-Hua (2003, <doi:10.1017/S0016672303006141>), and Wang Jing-Tian, Zhang Ya-Wen, Du Ying-Wen, Ren Wen-Long, Li Hong-Fu, Sun Wen-Xian, Ge Chao, and Zhang Yuan-Ming(2022, <doi:10.3724/SP.J.1006.2022.14088>)
Details
| Package: | SEA |
| Type: | Package |
| Version: | 2.0.1 |
| Date: | 2022-03-28 |
| Depends: | shiny,MASS,doParallel,foreach |
| Imports: | KScorrect,kolmim,utils,stats,grDevices,graphics,data.table |
| License: | GPL(>=2) |
| LazyLoad: | yes |
Users can use 'SEA()' start the GUI.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
References
The EIM algorithm in the joint segregation analysis of quantitative traits. Zhang Yuan-Ming*,Gai Junyi,Yang Yonghua(2003).
Examples
## Not run: SEA()
segregation analysis of BCF population
Description
Phenotypic observations in BCF population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
BCFFun(df,model,BCFtext2)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
BCFtext2 |
number of plants measured in each family. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
BCF=data(BCFexdata)
BCFFun(BCFexdata,"0MG",1)
BCF population dataset
Description
The phenotype of BCF population .
Usage
data(BCFexdata)
Details
Dataset input of BCFFun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of BC population
Description
Phenotypic observations in BC population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
BCFun(df,model)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
BC=data(BCexdata)
BCFun(BCexdata,"0MG")
BC population dataset
Description
The phenotype of BC population .
Usage
data(BCexdata)
Details
Dataset input of BCFun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of BIL population
Description
Phenotypic observations in BIL population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
BILFun(df,model,BILfr)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
BILfr |
BIL type. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
BIL=data(BILexdata)
BILFun(BILexdata,"0MG","BIL1(F1xP1)")
BIL population dataset
Description
The phenotype of BIL population .
Usage
data(BILexdata)
Details
Dataset input of BILFun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of DH population
Description
Phenotypic observations in DH population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
DHFun(df,model)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
DH=data(DHexdata)
DHFun(DHexdata,"0MG")
DH population dataset
Description
The phenotype of DH population .
Usage
data(DHexdata)
Details
Dataset input of DHFun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of F23 population
Description
Phenotypic observations in F23 population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
F23Fun(df,model,m_nf)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
m_nf |
number of plants measured in each family. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
F23=data(F23exdata)
F23Fun(F23exdata,"0MG",1)
F23 population dataset
Description
The phenotype of F23 population .
Usage
data(F23exdata)
Details
Dataset input of F23Fun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of F2 population
Description
Phenotypic observations in F2 population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
F2Fun(df,model)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
F2=data(F2exdata)
F2Fun(F2exdata,"0MG")
F2 population dataset
Description
The phenotype of F2 population .
Usage
data(F2exdata)
Details
Dataset input of F2Fun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of G3DH population
Description
Phenotypic observations in G3DH population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
G3DHFun(df,model,G3DHtext2)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
G3DHtext2 |
number of plants measured in each family. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G3DH=data(G3DHexdata)
G3DHFun(G3DHexdata,"0MG",1)
G3DH population dataset
Description
The phenotype of G3DH population .
Usage
data(G3DHexdata)
Details
Dataset input of G3DHFun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of G4F2 population
Description
Phenotypic observations in G4F2 population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
G4F2Fun(df,model)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G4F2=data(G4F2exdata)
G4F2Fun(G4F2exdata,"PG-AD")
G4F2 population dataset
Description
The phenotype of G4F2 population .
Usage
data(G4F2exdata)
Details
Dataset input of G4F2Fun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of G4F3 population
Description
Phenotypic observations in G4F3 population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
G4F3Fun(df,model,G4F3text2)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
G4F3text2 |
number of plants measured in each family. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G4F3=data(G4F3exdata)
G4F3Fun(G4F3exdata,"PG-AD",1)
G4F3 population dataset
Description
The phenotype of G4F3 population .
Usage
data(G4F3exdata)
Details
Dataset input of G4F3Fun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of G5BCF population
Description
Phenotypic observations in G5BCF population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
G5BCFFun(df,model,G5BCFtext2)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
G5BCFtext2 |
number of plants measured in each family. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G5BCF=data(G5BCFexdata)
G5BCFFun(G5BCFexdata,"1MG-AD",1)
G5BCF population dataset
Description
The phenotype of G5BCF population .
Usage
data(G5BCFexdata)
Details
Dataset input of G5BCFFun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of G5BC population
Description
Phenotypic observations in G5BC population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
G5BCFun(df,model)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G5BC=data(G5BCexdata)
G5BCFun(G5BCexdata,"1MG-AD")
G5BC population dataset
Description
The phenotype of G5BC population .
Usage
data(G5BCexdata)
Details
Dataset input of G5BCFun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of G5 population
Description
Phenotypic observations in G5 population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
G5Fun(df,model,G5text2)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
G5text2 |
number of plants measured in each family. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G5=data(G5exdata)
G5Fun(G5exdata,"PG-AD",1)
G5 population dataset
Description
The phenotype of G5 population .
Usage
data(G5exdata)
Details
Dataset input of G5Fun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of G6F population
Description
Phenotypic observations in G6F population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
G6FFun(df,model,G6Ftext2)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
G6Ftext2 |
number of plants measured in each family. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G6F=data(G6Fexdata)
G6FFun(G6Fexdata,"PG-AD",1)
G6F population dataset
Description
The phenotype of G6F population .
Usage
data(G6Fexdata)
Details
Dataset input of G6FFun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
segregation analysis of G6 population
Description
Phenotypic observations in G6 population have often been used to identify mixed major-gene plus polygene inheritance model for quantitative traits in plants.
Usage
G6Fun(df,model)
Arguments
df |
phenotype matrix. |
model |
genetic model. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G6=data(G6exdata)
G6Fun(G6exdata,"PG-AD")
G6 population dataset
Description
The phenotype of G6 population .
Usage
data(G6exdata)
Details
Dataset input of G6Fun function.
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Posterior Probability
Description
calculate posterior probability of the optimal model
Usage
PosPro(Population,result,data)Arguments
Population |
which Population to analysis. |
result |
result of calculation used corresponding population function. |
data |
phenotype matrix. |
Author(s)
Wang Jing-Tian, Zhang Ya-Wen, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
F23=data(F23exdata)
result<-F23Fun(F23exdata,"1MG-AD",1)
PosPro("F2:3",result,F23exdata)