qgtools (version 2.0)

ad.mq.jack: Additive-dominance (AD) model with MINQUE analysis and jackknife

Description

An AD model can be analyzed by MINQUE approach, requiring no specific genetic mating design or balance data. For reliable results, parents and F1s, parents and F2s, are preferred.

Usage

ad.mq.jack(Y, Ped, JacNum = NULL, JacRep = NULL)

Arguments

Y

A trait matrix including one or more traits.

Ped

A pedigree matrix including Env, Female, Male, Generation, with or without block is required. The matrix should include either 4 or 5 columns.

JacNum

Number of jackknife groups. The default is 10.

JacRep

Repeating times for jackknife process. The default is 1.

Value

Return a list of results: estimated Variance components, estimated proportional variance components, estimated fixed effects, and predicted random effects, and their statistical tests

Details

A pedigree matrix used for analysis is required in the order of Environment (column 1), Female(column 2), Male(column 3), Generation (column 4). Column 5 for block can be default. Even though there is only one environment, this column is needed.

References

Rao, C.R. 1971. Estimation of variance and covariance components-MINQUE theory. J Multiva Ana 1:19

Wu, J., McCarty Jr., J.C., Jenkins, J.N. 2010. Cotton chromosome substitution lines crossed with cultivars: Genetic model evaluation and seed trait analyses. Theoretical and Applied Genetics 120:1473-1483.

Wu, J., J. N. Jenkins, J. C. McCarty, K. Glover, and W. Berzonsky. 2010. Presentation titled by "Unbalanced Genetic Data Analysis: model evaluation and application" was offered at ASA, CSSA, & SSSA 2010 International Annual Meetings, Long Beach, CA.

Wu, J., J. N. Jenkins, and J.C., McCarty. 2011. A generalized approach and computer tool for quantitative genetics study. Proceedings Applied Statistics in Agriculture, April 25-27, 2010, Manhattan, KS. p.85-106.

Wu, J. 2012. GenMod: An R package for various agricultural data analyses. ASA, CSSA, and SSSA 2012 International Annual Meetings, Cincinnati, OH, p 127

Wu, J., Bondalapati K., Glover K., Berzonsky W., Jenkins J.N., McCarty J.C. 2013. Genetic analysis without replications: model evaluation and application in spring wheat. Euphytica. 190:447-458

Zhu, J. 1989. Estimation of Genetic Variance Components in the General Mixed Model. Ph.D. Dissertation, NC State University, Raleigh, U.S.A

Examples

# NOT RUN {
 data(cotf12)
 #names(cotf12)
 dat=cotf12[which(cotf12$Year==1),]
 Ped=dat[,c(1,3:6)]
 Y=dat[,-c(1:6)]
 res=ad.mq.jack(Y,Ped)
 res$Var
 res$PVar
 res$FixedEffect
 res$RandomEffect

 ##End
# }