sommer: DT_mohring – R documentation

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DT_mohring

Full diallel data for corn hybrids

Description

This dataset contains phenotpic data for 36 winter bean hybrids, coming from a full diallel design and evaluated for 9 traits. The column male and female origin columns are included as well.

Usage

data("DT_mohring")

Format

The format is: chr "DT_mohring"

Source

This data was generated by a winter bean study and originally included in the agridat package.

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

Examples

####=========================================####
#### For CRAN time limitations most lines in the
#### examples are silenced with one '#' mark,
#### remove them and run the examples
####=========================================####
data(DT_mohring)
DT <- DT_mohring
head(DT)
DT2 <- add.diallel.vars(DT,par1="Par1", par2="Par2")
head(DT2)

# GRIFFING MODEL 2 with reciprocal effects ###########################
mod1h <- mmer(Ftime ~ 1, data=DT2,
              random = ~ Block
              # GCA male & female overlayed
              + overlay(Par1, Par2) 
              # SCA effects (includes cross and selfs)
              + cross.id 
              # SCAR reciprocal effects (if zero there's no reciprocal effects)
              + cross.id:cross.type) 
summary(mod1h)$varcomp
##                                    VarComp VarCompSE   Zratio 
## Block.Ftime-Ftime                  0.00000   9.32181 0.000000 
## overlay(Par1, Par2).Ftime-Ftime 1276.73089 750.17269 1.701916 
## cross.id.Ftime-Ftime            1110.99090 330.16921 3.364914 
## cross.id:cross.type.Ftime-Ftime   66.02295  49.26876 1.340057 
## units.Ftime-Ftime                418.47949  74.56442 5.612321  
##
# GRIFFING MODEL 2, no reciprocal effects ##############################
mod1h <- mmer(Ftime ~ Block + is.cross, data=DT2,
              random = ~ 
              # GCA for all (female and male)
              overlay(Par1, Par2)  
              # GCA (only for hybrids)
              + overlay(Par1, Par2):is.cross  
              # SCA (hybrids only)
              + cross.id:is.cross) 
summary(mod1h)$varcomp
##                                           VarComp  VarCompSE   Zratio
## overlay(Par1, Par2).Ftime-Ftime          2304.1781 1261.63193 1.826347
## overlay(Par1, Par2):is.cross.Ftime-Ftime  613.6040  402.74347 1.523560
## cross.id:is.cross.Ftime-Ftime             340.7030  148.56225 2.293335
## units.Ftime-Ftime                         501.6275   74.36075 6.745864
##
# GRIFFING MODEL 3, no reciprocal effects ###############################
mod1h <- mmer(Ftime ~ Block + is.cross, data=DT2,
              random = ~ 
              # GCAC (only for hybrids)
              overlay(Par1, Par2):is.cross 
              # male GCA (only for inbreds)
              + Par1:is.self 
              # SCA (for hybrids only)
              + cross.id:is.cross) 
summary(mod1h)$varcomp
##                                           VarComp  VarCompSE   Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime  927.7895  537.91218 1.724797
## Par1:is.self.Ftime-Ftime                 9960.9247 5456.58188 1.825488
## cross.id:is.cross.Ftime-Ftime             341.4567  148.53667 2.298804
## units.Ftime-Ftime                         498.5974   73.92066 6.745035
##
# GRIFFING MODEL 2, with reciprocal effects #############################
# In Mohring: mixed model 3 reduced
mod1h <- mmer(Ftime ~ Block + is.cross, data=DT2,
              random = ~ 
              # GCAC (for hybrids only)
              overlay(Par1, Par2):is.cross 
              # male GCA (for selfs only)
              + Par1:is.self 
              # SCA (for hybrids only)
              + cross.id:is.cross 
              # SCAR reciprocal effects
              + cross.id:cross.type) 
summary(mod1h)$varcomp
##                                             VarComp  VarCompSE   Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime   927.78742  537.89981 1.724833
## Par1:is.self.Ftime-Ftime                 10001.78854 5456.47578 1.833013
## cross.id:is.cross.Ftime-Ftime              361.89712  148.54264 2.436318
## cross.id:cross.type.Ftime-Ftime             66.43695   49.24492 1.349113
## units.Ftime-Ftime                          416.82960   74.27202 5.612203
##
# GRIFFING MODEL 3, with RGCA + RSCA ####################################
# In Mohring: mixed model 3
mod1h <- mmer(Ftime ~ Block + is.cross, data=DT2,
              random = ~ 
              # GCAC (for hybrids only)
                overlay(Par1,Par2):is.cross 
              # RGCA: exclude selfs (to identify reciprocal effects)
              + overlay(Par1,Par2):cross.type 
              # male GCA (for selfs only)
              + Par1:is.self 
              # SCA (for hybrids only)
              + cross.id:is.cross 
              # SCAR: exclude selfs (if zero there's no reciprocal effects)
              + cross.id:cross.type) 
summary(mod1h)$varcomp
##                                            VarComp  VarCompSE    Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime   927.7843  537.88164 1.7248857
## Par1:is.self.Ftime-Ftime                 10001.7570 5456.30125 1.8330654
## cross.id:is.cross.Ftime-Ftime              361.8958  148.53670 2.4364068
## overlay(Par1, Par2):cross.type.Ftime-Ftime  17.9799   19.92428 0.9024114
## cross.id:cross.type.Ftime-Ftime             30.9519   46.43908 0.6665054
## units.Ftime-Ftime

sommer

Solving Mixed Model Equations in R

v4.1.3

GPL (>= 2)

Authors

Giovanny Covarrubias-Pazaran

Initial release

2021-04-01