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.
character; vector of the names of the markers
logical; TRUE, if the stacked data contains the all-negative row of markers; for example, TNFa-IL6-IL12-IFNa-
matrix of 0's and 1's; rows represent marker combinations, cols represent markers.
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.
N. Hawkins, Fred Hutchinson Cancer Research Center, Seattle, WA
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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