computeProfileData-methods: Method computeProfileData from Class "StackedData"

Description

This function is a method of the StackedData class which computes the profile data which can be stored in the profileData slot of a StackedData object. This method relies on the marker data slot being assigned in the StackedData object. No computation is required. Instead, the marker combination percentages data is re-organized to be 'horizontal' rather than 'stacked' (vertical). This makes it ready for plotting via the GroupListBoxplot() function.

Usage

computeProfileData(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

Methods

signature(object = "StackedData", byVarNames = "character", idVarName = "character", percentVarName = "character", groupVarName = "character"): Compute the profile 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 profile percent data and set the profile percent data slot
byVarNames = c("stim", "concGroup", "cell")
profilePercent = computeProfileData(stackedDataObject, byVarNames, "id", "percentAll", "group")
profileData(stackedDataObject) = profilePercent