computePFDData-methods {flowPlots} | R Documentation |
This function is a method of the StackedData class which computes the polyfunctional degree (pfd) data (usually recorded as percentages of reactive cells) which can be stored in the pfdData slot of a StackedData object. PFD=1 refers to cells which are producing only one marker. PFD=2 refers to cells which are producing exactly two markers. Similarly, up to PFD=n, where n is the number of markers. This method relies on the marker data slot being assigned in the StackedData object.
computePFDData(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 |
data frame of pfd data
signature(object = "StackedData", byVarNames = "character", idVarName = "character", percentVarName = "character", groupVarName = "character")
Computes the pfd 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 data and set the pfd data slot byVarNames = c("stim", "concGroup", "cell") pfdData = computePFDData(stackedDataObject, byVarNames, "id", "percentAll", "group") pfdData(stackedDataObject) = pfdData