computePFDData-methods: Method computePFDData from Class "StackedData"

In flowPlots: flowPlots: analysis plots and data class for gated flow cytometry data

Description

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.

Usage

   computePFDData(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

data frame of pfd data

Methods

signature(object = "StackedData", byVarNames = "character", idVarName = "character", percentVarName = "character", groupVarName = "character")

Computes the pfd data.

Author(s)

N. Hawkins, Fred Hutchinson Cancer Research Center, Seattle, WA

See Also

StackedData, pfdData

Examples

# 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
 

flowPlots documentation built on Nov. 8, 2020, 7:54 p.m.