computePFDPartsData-methods: Method computePFDPartsData 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 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.

Author(s)

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

See Also

StackedData, pfdPartsData

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

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