DT_mohring: Full diallel data for corn hybrids
In sommer: Solving Mixed Model Equations in R
DT_mohring R Documentation
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
See Also
The core functions of the package mmer and mmec
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)
# # is.cross denotes a hybrid (1)
# # is.self denotes an inbred (1)
# # cross.type denotes one way (-1, e.g. AxB) and reciprocal (1, e.g., BxA) and no cross (0)
# # cross.id denotes the name of the cross (same name for direct & reciprocal)
#
# # 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 (remaining variance in crosses;
# # if zero there's no reciprocal effects)
# + cross.id:cross.type)
# summary(mod1h)$varcomp
#
# mod1hb <- mmec(Ftime ~ 1, data=DT2,
# random = ~ Block
# # GCA male & female overlayed
# + vsc(isc(overlay(Par1, Par2)))
# # SCA effects (includes cross and selfs)
# + cross.id
# # SCAR reciprocal effects (remaining variance in crosses;
# # if zero there's no reciprocal effects)
# + vsc(dsc(cross.type), isc(cross.id)) )
# summary(mod1hb)$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 effect for all (hybrids and inbreds)
# overlay(Par1, Par2)
# # GCA effect (calculated only in hybrids; remaining variance)
# + overlay(Par1, Par2):is.cross
# # SCA effect (calculated in hybrids only)
# + cross.id:is.cross)
# summary(mod1h)$varcomp
#
# mod1h <- mmec(Ftime ~ Block + is.cross, data=DT2, nIters = 50,
# random = ~
# # GCA effects for all (hybrids and inbreds)
# vsc(isc(overlay(Par1, Par2)))
# # GCA effect (calculated only in hybrids; remaining variance)
# + vsc(isc(is.cross),isc(overlay(Par1, Par2)))
# # SCA effect (calculated in hybrids only)
# + vsc(isc(is.cross), isc(cross.id))
# )
# summary(mod1h)$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)$varcomp
#
# mod1h <- mmec(Ftime ~ Block + is.cross, data=DT2, nIters = 100,
# random = ~
# # GCAC (only for hybrids)
# vsc(isc(is.cross),isc(overlay(Par1, Par2)))
# # male GCA (only for inbreds)
# + vsc(isc(is.self),isc(Par1))
# # SCA (for hybrids only)
# + vsc(isc(is.cross), isc(cross.id))
# )
# summary(mod1h)$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 (remaning SCA variance)
# + cross.id:cross.type)
# summary(mod1h)$varcomp
#
# mod1h <- mmec(Ftime ~ Block + is.cross, data=DT2, nIters = 100,
# random = ~
# # GCAC (for hybrids only)
# vsc(isc(is.cross),isc(overlay(Par1, Par2)))
# # male GCA (for selfs only)
# + vsc(isc(is.self),isc(Par1))
# # SCA (for hybrids only)
# + vsc(isc(is.cross), isc(cross.id))
# # SCAR reciprocal effects (remaning SCA variance)
# + vsc(isc(cross.type), isc(cross.id))
# )
# summary(mod1h)$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 GCA 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 SCA effects)
# + cross.id:cross.type)
# summary(mod1h)$varcomp
#
# mod1h <- mmec(Ftime ~ Block + is.cross, data=DT2,nIters = 100,
# random = ~
# # GCAC (for hybrids only)
# vsc(isc(is.cross),isc(overlay(Par1, Par2)))
# # RGCA: exclude selfs (to identify reciprocal GCA effects)
# + vsc(isc(cross.type),isc(overlay(Par1, Par2)))
# # male GCA (for selfs only)
# + vsc(isc(is.self),isc(Par1))
# # SCA (for hybrids only)
# + vsc(isc(is.cross), isc(cross.id))
# # SCAR: exclude selfs (if zero there's no reciprocal SCA effects)
# + vsc(isc(cross.type), isc(cross.id))
# )
# summary(mod1h)$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 416.09922 447.2101 0.93043333
sommer documentation built on Sept. 11, 2024, 6:22 p.m.
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| DT_mohring | R Documentation |
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
See Also
The core functions of the package mmer and mmec
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)
# # is.cross denotes a hybrid (1)
# # is.self denotes an inbred (1)
# # cross.type denotes one way (-1, e.g. AxB) and reciprocal (1, e.g., BxA) and no cross (0)
# # cross.id denotes the name of the cross (same name for direct & reciprocal)
#
# # 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 (remaining variance in crosses;
# # if zero there's no reciprocal effects)
# + cross.id:cross.type)
# summary(mod1h)$varcomp
#
# mod1hb <- mmec(Ftime ~ 1, data=DT2,
# random = ~ Block
# # GCA male & female overlayed
# + vsc(isc(overlay(Par1, Par2)))
# # SCA effects (includes cross and selfs)
# + cross.id
# # SCAR reciprocal effects (remaining variance in crosses;
# # if zero there's no reciprocal effects)
# + vsc(dsc(cross.type), isc(cross.id)) )
# summary(mod1hb)$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 effect for all (hybrids and inbreds)
# overlay(Par1, Par2)
# # GCA effect (calculated only in hybrids; remaining variance)
# + overlay(Par1, Par2):is.cross
# # SCA effect (calculated in hybrids only)
# + cross.id:is.cross)
# summary(mod1h)$varcomp
#
# mod1h <- mmec(Ftime ~ Block + is.cross, data=DT2, nIters = 50,
# random = ~
# # GCA effects for all (hybrids and inbreds)
# vsc(isc(overlay(Par1, Par2)))
# # GCA effect (calculated only in hybrids; remaining variance)
# + vsc(isc(is.cross),isc(overlay(Par1, Par2)))
# # SCA effect (calculated in hybrids only)
# + vsc(isc(is.cross), isc(cross.id))
# )
# summary(mod1h)$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)$varcomp
#
# mod1h <- mmec(Ftime ~ Block + is.cross, data=DT2, nIters = 100,
# random = ~
# # GCAC (only for hybrids)
# vsc(isc(is.cross),isc(overlay(Par1, Par2)))
# # male GCA (only for inbreds)
# + vsc(isc(is.self),isc(Par1))
# # SCA (for hybrids only)
# + vsc(isc(is.cross), isc(cross.id))
# )
# summary(mod1h)$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 (remaning SCA variance)
# + cross.id:cross.type)
# summary(mod1h)$varcomp
#
# mod1h <- mmec(Ftime ~ Block + is.cross, data=DT2, nIters = 100,
# random = ~
# # GCAC (for hybrids only)
# vsc(isc(is.cross),isc(overlay(Par1, Par2)))
# # male GCA (for selfs only)
# + vsc(isc(is.self),isc(Par1))
# # SCA (for hybrids only)
# + vsc(isc(is.cross), isc(cross.id))
# # SCAR reciprocal effects (remaning SCA variance)
# + vsc(isc(cross.type), isc(cross.id))
# )
# summary(mod1h)$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 GCA 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 SCA effects)
# + cross.id:cross.type)
# summary(mod1h)$varcomp
#
# mod1h <- mmec(Ftime ~ Block + is.cross, data=DT2,nIters = 100,
# random = ~
# # GCAC (for hybrids only)
# vsc(isc(is.cross),isc(overlay(Par1, Par2)))
# # RGCA: exclude selfs (to identify reciprocal GCA effects)
# + vsc(isc(cross.type),isc(overlay(Par1, Par2)))
# # male GCA (for selfs only)
# + vsc(isc(is.self),isc(Par1))
# # SCA (for hybrids only)
# + vsc(isc(is.cross), isc(cross.id))
# # SCAR: exclude selfs (if zero there's no reciprocal SCA effects)
# + vsc(isc(cross.type), isc(cross.id))
# )
# summary(mod1h)$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 416.09922 447.2101 0.93043333
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