pcvr (version 1.2.0)

relativeTolerance: Calculate relative tolerance of some phenotype(s) relative to control

Description

Often in bellwether experiments we are curious about the effect of some treatment vs control. For certain routes in analysing the data this requires considering phenotypes as relative differences compared to a control. Note that the conjugate function can also be useful in considering the relative tolerance to stress between groups and that growth models are another suggested way to test relative tolerance questions.

Usage

relativeTolerance(
  df,
  phenotypes = NULL,
  grouping = NULL,
  control = NULL,
  controlGroup = NULL,
  traitCol = "trait",
  valueCol = "value"
)

Value

A dataframe with relative tolerance columns added.

Arguments

df

Dataframe to use, this can be in long or wide format.

phenotypes

A character vector of column names for the phenotypes that should be compared against control.

grouping

A character vector of column names that identify groups in the data. These groups will be calibrated separately, with the exception of the group that identifies a control within the greater hierarchy. Note that for levels of grouping where the control group does not exist the output will be NA.

control

A column name for the variable to be used to select the control observations. If left NULL (the default) then this will be taken as the first string in the group argument.

controlGroup

The level of the control variable to compare groups against.

traitCol

Column with phenotype names, defaults to "trait". This should generally not need to be changed from the default. If this and valueCol are present in colnames(df) then the data is assumed to be in long format.

valueCol

Column with phenotype values, defaults to "value". This should generally not need to be changed from the default.

Examples

# \donttest{
f <- "https://raw.githubusercontent.com/joshqsumner/pcvrTestData/main/pcv4-single-value-traits.csv"
tryCatch(
  {
    sv <- read.pcv(
      f,
      reader = "fread"
    )
    sv$genotype <- substr(sv$barcode, 3, 5)
    sv$genotype <- ifelse(sv$genotype == "002", "B73",
      ifelse(sv$genotype == "003", "W605S",
        ifelse(sv$genotype == "004", "MM", "Mo17")
      )
    )
    sv$fertilizer <- substr(sv$barcode, 8, 8)
    sv$fertilizer <- ifelse(sv$fertilizer == "A", "100",
      ifelse(sv$fertilizer == "B", "50", "0")
    )

    sv <- bw.time(sv,
      plantingDelay = 0, phenotype = "area_pixels",
      cutoff = 10, timeCol = "timestamp", group = c("barcode", "rotation"), plot = FALSE
    )
    phenotypes <- colnames(sv)[19:35]
    phenoForm <- paste0("cbind(", paste0(phenotypes, collapse = ", "), ")")
    groupForm <- "DAS+DAP+barcode+genotype+fertilizer"
    form <- as.formula(paste0(phenoForm, "~", groupForm))
    sv <- aggregate(form, data = sv, mean, na.rm = TRUE)
    sv <- bw.outliers(sv,
      phenotype = "area_pixels",
      group = c("DAS", "genotype", "fertilizer"),
      plotgroup = c("barcode")
    )$data

    pixels_per_cmsq <- 42.5^2 # pixel per cm^2
    sv$area_cm2 <- sv$area_pixels / pixels_per_cmsq
    sv$height_cm <- sv$height_pixels / 42.5

    df <- sv
    phenotypes <- c("area_cm2", "height_cm")
    grouping <- c("fertilizer", "genotype", "DAS")
    controlGroup <- "100"
    control <- "fertilizer"

    rt <- relativeTolerance(df, phenotypes, grouping, control, controlGroup)
    head(rt)
    sapply(rt, function(c) sum(is.na(c)))
  },
  error = function(e) {
    message(e)
  }
)
# }