computePFDPartsData-methods: Method computePFDPartsData from Class "StackedData"

Description

This function is a method of the StackedData class which computes the pfdParts data which can be stored in the pfdPartsData slot of a StackedData object. This method relies on the marker data slot being assigned in the StackedData object.

Usage

computePFDPartsData(object, byVarNames, idVarName, percentVarName, groupVarName)

Arguments

object

an object of the StackedData class

byVarNames

character; the names of the variables specifying the subsets of interest in the data

idVarName

character; the name of the id variable in the data

percentVarName

character; the name of the variable holding the percentages to be summed when computing the pfd summary data

groupVarName

character; the name of the variable specifying the group assignment in the data

Value

a list. Each element of the list is a data frame containing the component percents for a given degree of polyfunctionality (PFD), except for the max PFD since there is only one possible combination for the max PFD.

Methods

signature(object = "StackedData", byVarNames = "character", idVarName = "character", percentVarName = "character", groupVarName = "character"): Compute the pfd parts data.

Examples

Run this code

# Load stacked data
data(adultsNeonates)
# Create a stacked data object
stackedDataObject = new("StackedData", stackedData=adultsNeonates)

# Compute the marker data and set the marker data slot
markerNames = c("TNFa","IL6","IL12","IFNa")
markers = computeMarkers(markerNames,includeAllNegativeRow=TRUE)
markers(stackedDataObject) = markers

# Compute the pfd parts data and set the pfd parts data slot
byVarNames = c("stim", "concGroup", "cell")
pfdPartsData = computePFDPartsData(stackedDataObject, byVarNames, "id", "percentAll", "group")
pfdPartsData(stackedDataObject) = pfdPartsData