computePFDPartsData-methods {flowPlots} | R Documentation |
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.
computePFDPartsData(object, byVarNames, idVarName, percentVarName, groupVarName)
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 |
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.
signature(object = "StackedData", byVarNames = "character", idVarName = "character", percentVarName = "character", groupVarName = "character")
Compute the pfd parts data.
N. Hawkins, Fred Hutchinson Cancer Research Center, Seattle, WA
# 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