COMPASS                 Fit the COMPASS Model
COMPASS-package         COMPASS (Combinatorial Polyfunctionality
                        Analysis of Single-Cells)
COMPASSContainer        Generate the Data Object used by COMPASS
COMPASSContainer-data   Simulated COMPASSContainer
COMPASSContainerFromGatingSet
                        Create a COMPASS Container from a GatingSet
COMPASSDescription      Get and Set the Description for the Shiny
                        Application
COMPASSMCMCDiagnosis    Diagnostic of a set of COMPASS Models.
COMPASSResult-accessors
                        COMPASSResult Accessors
COMPASSResult-data      Simulated COMPASS fit
COMPASSfitToCountsTable
                        Extract a table of counts from a COMPASSResult
                        object
CellCounts              Compute Number of Cells Positive for Certain
                        Cytokine Combinations
Combinations            Generate Combinations
FunctionalityScore      Compute the Functionality Score for each
                        subject fit in a COMPASS model
GetThresholdedIntensities
                        Extract Thresholded Intensities from a
                        GatingSet
PolyfunctionalityScore
                        Compute the Polyfunctionality Score for each
                        subject fit in a COMPASS model
Posterior               Retrieve Posterior Measures from a COMPASS fit
Response                Compute a response probability from COMPASS
                        mcmc samples.
SimpleCOMPASS           Fit the discrete COMPASS Model
TotalCellCounts         Compute Total Cell Counts
UniqueCombinations      Generate Unique Combinations
categories              Categories
getCounts               Get a data.table of counts of polyfunctional
                        subsets
markers                 Markers
melt_                   Make a 'Wide' data set 'Long'
merge.COMPASSContainer
                        Merge Two COMPASSContainers
metadata                Metadata
pheatmap                A function to draw clustered heatmaps.
plot.COMPASSResult      Plot a COMPASSResult
plot2                   Plot a pair of COMPASSResults
plotCOMPASSResultStack
                        Plot multiple COMPASSResults
print.COMPASSContainer
                        Print a COMPASSContainer Object
print.COMPASSResult     Print a COMPASSResult Object
scores                  Fetch the table of scores and metadata from a
                        COMPASSResult Object
select_compass_pops     Flag COMPASS boolean populations
shinyCOMPASS            Start a Shiny Application for Visualizing
                        COMPASS Results
shinyCOMPASSDeps        List Shiny Dependencies
subset.COMPASSContainer
                        Subset a COMPASSContainer
summary.COMPASSContainer
                        Summarize a COMPASSContainer Object
summary.COMPASSResult   Summarize a COMPASSResult Object
translate_marker_names
                        Translate marker names to format use by COMPASS
transpose_list          Transpose a List
