StackedData-class: Class "StackedData"

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

Description

Stacked data refers to gated data originating from an ICS Flow Cytometry experiment where the marker combinations for a subset of interest, say a given cell type, stimulus, and concentration, are "stacked". A common type of marker is a cytokine. A subset of stacked data could look like this:

   id   group stim concGroup cell percentAll count totalCount percentReactive            cytCombo

a2004 	adult  LPS         3  mDC       0.00     0        700        0.000000 TNFa+IL6+IL12+IFNa+

a2004 	adult  LPS         3  mDC       0.43     3        700        0.940625 TNFa+IL6+IL12+IFNa-

a2004 	adult  LPS         3  mDC       0.00     0        700        0.000000 TNFa+IL6+IL12-IFNa+

a2004 	adult  LPS         3  mDC      21.86   153        700       47.818750 TNFa+IL6+IL12-IFNa-

a2004 	adult  LPS         3  mDC       0.00     0        700        0.000000 TNFa+IL6-IL12+IFNa+

a2004 	adult  LPS         3  mDC       0.29     2        700        0.634375 TNFa+IL6-IL12+IFNa-

a2004 	adult  LPS         3  mDC       0.00     0        700        0.000000 TNFa+IL6-IL12-IFNa+

a2004 	adult  LPS         3  mDC      19.71   138        700       43.115625 TNFa+IL6-IL12-IFNa-

Details

The marker combinations in the stacked data should be ordered within each subset of interest (for example: subjectID, celltype, concentration, and stimulation) to match the marker matrix. If the data are not in this order, it should be sorted into this order before using the computeProfileData, computeMarginalData, computePFDData, computePFDPartsData methods. The computeMarkers method can be used to compute the marker matrix used by these methods. If the matrix computed does not match the order of your data, then you can supply your own marker matrix, assign it to the marker data slot of a StackedData object, and then use the 'compute' methods to compute the other types of data.

Objects from the Class

Objects can be created by calls of the form:

stackedDataObject = new("StackedData", stackedData=NA, profileData=NA, marginalData=NA, pfdData=NA, pfdPartsData=NA, markers=NA )

Slots

stackedData:

"data.frame" of stacked data

profileData:

"data.frame" of profile data

marginalData:

"data.frame" of marginal data

pfdData:

"data.frame" of pfd data

pfdPartsData:

"list" of "data.frame" 's of pfd parts data

markers:

"matrix" of marker data

Methods

computeMarginalData

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

computeMarkers

signature(markerNames = "character", includeAllNegativeRow = "logical")

computePFDData

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

computePFDPartsData

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

computeProfileData

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

# getters

marginalData

signature(object = "StackedData")

markers

signature(object = "StackedData")

pfdData

signature(object = "StackedData")

pfdPartsData

signature(object = "StackedData")

profileData

signature(object = "StackedData")

stackedData

signature(object = "StackedData")

# setters

marginalData

signature(object = "StackedData", value = "data.frame")

markers

signature(object = "StackedData", value = "matrix")

pfdData

signature(object = "StackedData", value = "data.frame")

pfdPartsData

signature(object = "StackedData", value = "list")

profileData

signature(object = "StackedData", value = "data.frame")

stackedData

signature(object = "StackedData", value = "data.frame")

Author(s)

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

See Also

markers, profileData, marginalData, pfdData, pfdPartsData, adultsNeonates

Examples

# View the Data Slots in StackedData
showClass("StackedData")

# 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
# The marker matrix computed here matches the order of the marker combinations
# in the adultsNeonates stacked data within each subset of interest
markerNames = c("TNFa","IL6","IL12","IFNa")
markers = computeMarkers(markerNames,includeAllNegativeRow=TRUE)
markers(stackedDataObject) = markers

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

# Compute the marginal data and set the marginal data slot
byVarNames = c("stim", "concGroup", "cell")
marginalData = computeMarginalData(stackedDataObject, byVarNames, "id", "percentAll", "group")
marginalData(stackedDataObject) = marginalData

# 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

# 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

# Get the data from the stacked data object

markers = markers(stackedDataObject)
profileData = profileData(stackedDataObject)
marginalData = marginalData(stackedDataObject)
pfdData = pfdData(stackedDataObject)
pfdPartsData = pfdPartsData(stackedDataObject)

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