getGenoPred: Extract predicted genotypic values

In statgenHTP: High Throughput Phenotyping (HTP) Data Analysis

Extract predicted genotypic values

Description

Extract predictions of the genotypic value from an object of class fitMod.

Usage

getGenoPred(
  fitMod,
  timePoints = names(fitMod),
  predictChecks = FALSE,
  outFile = NULL
)

Arguments

fitMod	An object of class fitMod.
timePoints	A character or numeric vector indicating the time point(s) for which the predictions should be extracted. When using a character string to reference a time point, the value has to be an exact match to one of the existing time points. When using a number it will be matched by its number ("timeNumber") in the timePoints attribute of the TP object.
predictChecks	Should predictions of the check genotypes be included in the ouptut. If TRUE a list of two data.frames is returned from the function, one with the predictions for the regular genotypes and one with the predictions for the checks.
outFile	A character string indicating the .csv file to which the results should be written. If NULL no file is written.

Value

A list of two data.frames with predicted genotypic values per time point. genoPred with the predicted values for the genotypes and checkPred with the predicted values for the checks. If predictChecks = FALSE the latter will be NULL.

See Also

Other functions for spatial modeling: fitModels(), getCorrected(), getEffDims(), getHerit(), getVar(), plot.fitMod(), summary.fitMod()

Examples

## Using the first example dataset (PhenovatorDat1).

phenoTP <- createTimePoints(dat = PhenovatorDat1,
                            experimentName = "Phenovator",
                            genotype = "Genotype",
                            timePoint = "timepoints",
                            repId = "Replicate",
                            plotId = "pos",
                            rowNum = "y", colNum = "x",
                            addCheck = TRUE,
                            checkGenotypes = c("check1", "check2",
                                               "check3", "check4"))

## Fit a SpATS model on few time points.
modPhenoSp <- fitModels(TP = phenoTP,
                        trait = "EffpsII",
                        timePoints = c(1, 6, 20))

## Extract the genotypic predictions for one time point:
genoPredSp <- getGenoPred(modPhenoSp,
                          timePoints = 6)
head(genoPredSp)

statgenHTP documentation built on April 14, 2023, 9:12 a.m.