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Create an object of class TP

Source: R/createTimePoints.R
createTimePoints.Rd

Convert a data.frame to an object of class TP (Time Points). The function converts a data.frame to an object of class TP in the following steps:

  • Quality control on the input data. For example, warnings will be given when more than 50% of observations are missing for a plant.

  • Rename columns to default column names used by the functions in the statgenHTP package. For example, the column in the data containing variety/accession/genotype is renamed to “genotype.” Original column names are stored as an attribute of the individual data.frames in the TP object.

  • Convert column types to the default column types. For example, the column “genotype” is converted to a factor and “rowNum” to a numeric column.

  • Convert the column containing time into time format. If needed, the time format can be provided in timeFormat. For example, with a date/time input of the form “day/month/year hour:minute”, use "%d/%m/%Y %H:%M". For a full list of abbreviations see the R package strptime. When the input time is a numeric value, the function will convert it to time from 01-01-1970.

  • If addCheck = TRUE, the genotypes listed in checkGenotypes are reference genotypes (or check). It will add a column check with a value "noCheck" for the genotypes that are not in checkGenotypes and the name of the genotypes for the checkGenotypes. A column genoCheck is also added with the names of the genotypes that are not in checkGenotypes and NA for the checkGenotypes. These columns are necessary for fitting models on data that includes check genotypes, e.g. reference genotypes that are highly replicated or in case of augmented design.

  • Split the data into separate data.frames by time point. A TP object is a list of data.frames where each data.frame contains the data for a single time point. If there is only one time point the output will be a list with only one item.

  • Add a data.frame with columns timeNumber and timePoint as attribute “timePoints” to the TP object. This data.frame can be used for referencing time points by a unique number.

Note that plotId needs to be a unique identifier for a plot or a plant. It cannot occur more than once per time point.

Usage

createTimePoints(
  dat,
  experimentName,
  genotype,
  timePoint,
  timeFormat = NULL,
  plotId,
  repId = NULL,
  rowNum = NULL,
  colNum = NULL,
  addCheck = FALSE,
  checkGenotypes = NULL
)

Arguments

dat

A data.frame.

experimentName

A character string, the name of the experiment. Stored with the data and used in default plot titles.

genotype

A character string indicating the column in dat containing the genotypes.

timePoint

A character string indicating the column in dat containing the time points.

timeFormat

A character string indicating the input format of the time points. E.g. for a date/time input of the form day/month/year hour:minute, use "%d/%m/%Y %H:%M". For a full list of abbreviations see strptime. If NULL, a best guess is done based on the input.

plotId

A character string indicating the column in dat containing the plotId. This has to be a unique identifier per plot/plant per time point.

repId

A character string indicating the column in dat containing the replicates.

rowNum

A character string indicating the column in dat containing the row number of the plot.

colNum

A character string indicating the column in dat containing the column number of the plot.

addCheck

Should a column check be added to the output? If TRUE, checkGenotypes cannot be NULL.

checkGenotypes

A character vector containing the genotypes used as checks in the experiment.

Value

An object of class TP. A list with, per time point in the input, a data.frame containing the data for that time point. A data.frame with columns timeNumber and timePoint is added as attribute timePoints to the data. This data.frame can be used for referencing timePoints by their number.

See also

Other functions for data preparation: as.data.frame.TP(), getTimePoints(), plot.TP(), removeTimePoints(), summary.TP()

Examples

## Create a TP object containing the data from the Phenovator.
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"))
#> Warning: The following plotIds have observations for less than 50% of the time points:
#> c24r41, c7r18, c7r49
summary(phenoTP)
#> phenoTP contains data for experiment Phenovator.
#> 
#> It contains 73 time points.
#> First time point: 2018-05-31 16:37:00 
#> Last time point: 2018-06-18 16:37:00 
#> 
#> The following genotypes are defined as check genotypes: check1, check2, check3, check4.