Method computeMarkers from Class "StackedData"

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Description

This function is a method of the StackedData class which computes the markers which can be stored in the markers data slot of a StackedData object. The marker matrix should match the order of the rows in the stacked data file. The stacked data should be sorted so that the order of each 'stack' in the file is the same. This method can be used to compute a marker matrix. If that matrix does not match the order of the 'stack', then the user can generate the marker matrix separately and assign it to the marker the data slot in a StackedData object.

Usage

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   computeMarkers(markerNames, includeAllNegativeRow)    

Arguments

markerNames

character; vector of the names of the markers

includeAllNegativeRow

logical; TRUE, if the stacked data contains the all-negative row of markers; for example, TNFa-IL6-IL12-IFNa-

Value

matrix of 0's and 1's; rows represent marker combinations, cols represent markers.

Methods

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

Compute the markers. Include the all negative row if the data includes the all negative case, such as: TNFa-IFNg-IL2-, in this case with 3 markers.

Author(s)

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

See Also

StackedData, markers

Examples

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# Compute the marker data
markerNames = c("TNFa","IL6","IL12","IFNa")
markers = computeMarkers(markerNames,includeAllNegativeRow=TRUE)

## If you're using a StackedData object to compute summary data

# Create a stacked data object
stackedDataObject = new("StackedData")

# Assign the markers to the marker data slot
markers(stackedDataObject) = markers

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