computeProfileData-methods: Method computeProfileData 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 profile data which can be stored in the profileData slot of a StackedData object. This method relies on the marker data slot being assigned in the StackedData object. No computation is required. Instead, the marker combination percentages data is re-organized to be 'horizontal' rather than 'stacked' (vertical). This makes it ready for plotting via the GroupListBoxplot() function.

Usage

   computeProfileData(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 profile data

Methods

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

Compute the profile data.

Author(s)

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

See Also

StackedData, profileData

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 profile percent data and set the profile percent data slot
byVarNames = c("stim", "concGroup", "cell")
profilePercent = computeProfileData(stackedDataObject, byVarNames, "id", "percentAll", "group")
profileData(stackedDataObject) = profilePercent

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