The Genotype plus Genotype by Environment interaction (GGE) model fits
a model with trial as main fixed effect. Then a principal component
analysis is done on the residuals. This results in an interaction
characterized by Interaction Principal Components (IPCA)
enabling simultaneous plotting of genotypes and trials.
The parameter nPC
is used to indicate the number of principal
components that is used in the principal component analysis (PCA). By setting
this parameter to NULL
the algorithm determines the best number of
principal components (see Details).
By specifying the parameter byYear = TRUE
, a separate analysis will be
done for every year in the data. Combining the option with nPC = NULL
may result in different numbers of principal components per year. The GGE
estimates will still be returned as a single data.frame, but the other
results will be either lists or arrays.
Usage
gxeGGE(
TD,
trials = names(TD),
trait,
nPC = 2,
byYear = FALSE,
center = TRUE,
excludeGeno = NULL,
useWt = FALSE
)
Arguments
- TD
An object of class
TD
.- trials
A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.
- trait
A character string specifying the trait to be analyzed.
- nPC
An integer specifying the number of principal components used as multiplicative term of genotype-by-trial interaction. If
NULL
, the number of principal components is determined by the algorithm using forward selection. See details.- byYear
Should the analysis be done by year? If
TRUE
the data is split by the variable year, analysis is performed and the results are merged together and returned.- center
Should the variables be shifted to be zero centered?
- excludeGeno
An optional character vector with names of genotypes to be excluded from the analysis. If
NULL
, all genotypes are used.- useWt
Should weighting be used when modeling? Requires a column
wt
inTD
.
Details
First a linear model \(trait = trial + \epsilon\) is fitted with trial a
fixed component in the model.
The residuals from the fitted model are then used in a PCA. If nPC
is
not NULL
a single PCA is done using prcomp
with
maximum rank nPC
.
In case nPC = NULL
, the PCA is first done with one PC. Then using
forward selection one by one the number of PCs is increased as long as the
added component is significant in the analysis.
GGE estimates are then computed using the results of the PCA.