Replace outliers for single observations by NA

Function for replacing outliers for single observations by NA.

Usage

removeSingleOut(TP, singleOut, trait = attr(x = singleOut, which = "trait"))

Arguments

TP

An object of class TP.

singleOut

A data.frame with at least the columns plotId and timePoint with values corresponding to those in TP. If a column outlier is present, as in the output of detectSingleOut, only plotId x timePoint combinations for which outlier = 1 will be set to NA. If no column outlier is present, all observations in singleOut will be set to NA.

trait

The trait that should be set to NA. Can be ignored when using the output of detectSingleOut as input.

Value

An object of class TP, the input with the outlier replaced by NA.

See also

Other functions for detecting outliers for single observations: detectSingleOut(), detectSingleOutMaize(), plot.singleOut()

Examples

## Create a TP object containing the data from the Phenovator.
PhenovatorDat1 <- PhenovatorDat1[!PhenovatorDat1$pos %in%
                                 c("c24r41", "c7r18", "c7r49"), ]
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"))

## First select a subset of plants, for example here 9 plants.
plantSel <- phenoTP[[1]]$plotId[1:9]
# Then run on the subset
resuVatorHTP <- detectSingleOut(TP = phenoTP,
                                trait = "EffpsII",
                                plotIds = plantSel,
                                confIntSize = 3,
                                nnLocfit = 0.1)

## Replace the studied trait by NA for the plants marked as outliers.
phenoTPOut <- removeSingleOut(phenoTP, resuVatorHTP)