removeSerieOut: Replace outliers for series of observations by NA

In statgenHTP: High Throughput Phenotyping (HTP) Data Analysis

Replace outliers for series of observations by NA

Description

Function for replacing outliers for series of observations in the data by NA. The input can either be a data.frame, specified in dat, or the output of the fitSpline function, specified in fitSpline. Exactly one of these should be provided as input for the function.

Usage

removeSerieOut(
  dat = NULL,
  fitSpline = NULL,
  serieOut,
  reason = c("mean corr", "angle", "slope"),
  traits = attr(x = serieOut, which = "trait")
)

Arguments

dat	A data.frame.
fitSpline	An object of class HTPSpline, the output of the fitSpline function.
serieOut	A data.frame with at least the column plotId with values corresponding to those in dat/fitSpline.
reason	A character vector indicating which types of outliers should be replaced by NA.
traits	The traits that should be replaced by NA. When using the output of detectSerieOut as input for serieOut this defaults to the trait used for when detecting the outliers.

Value

Depending on the input either a data.frame or an object of class HTPSpline for which the outliers specified in serieOut are replaced by NA.

See Also

Other functions for detecting outliers for series of observations: detectSerieOut(), plot.serieOut()

Examples

## Run the function to fit P-splines on a subset of genotypes.
subGenoVator <- c("G160", "G151")
fit.spline <- fitSpline(inDat = spatCorrectedVator,
                        trait = "EffpsII_corr",
                        genotypes = subGenoVator,
                        knots = 50)

## Extract the tables of predicted values and P-spline coefficients.
predDat <- fit.spline$predDat
coefDat <- fit.spline$coefDat

## The coefficients are then used to tag suspect time courses
outVator <- detectSerieOut(corrDat = spatCorrectedVator,
                           predDat = predDat,
                           coefDat = coefDat,
                           trait = "EffpsII_corr",
                           genotypes = subGenoVator,
                           thrCor = 0.9,
                           thrPca = 30,
                           thrSlope = 0.7)

## Replace the outliers by NA in the corrected data.
spatCorrectedVatorOut <- removeSerieOut(dat = spatCorrectedVator,
                                        serieOut = outVator)

## Only replace the slope outliers by NA in the corrected data.
spatCorrectedVatorOut2 <- removeSerieOut(dat = spatCorrectedVator,
                                        serieOut = outVator,
                                        reason = "slope")

## Replace the outliers by NA in the corrected data.
## Replace both the corrected value and the raw trait value by NA.
spatCorrectedVatorOut3 <-
  removeSerieOut(dat = spatCorrectedVator,
                 serieOut = outVator,
                 traits = c("EffpsII", "EffpsII_corr"))

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