computePFDData-methods: Method computePFDData from Class "StackedData"

Description Usage Arguments Value Methods Author(s) See Also Examples

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

1
   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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
# 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.