# Combinatorial Polyfunctionality Analysis of Single Cells

## Documentation for package ‘COMPASS’ version 1.28.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

COMPASS-package | COMPASS (Combinatorial Polyfunctionality Analysis of Single-Cells)
categories | Categories
CC | Simulated COMPASSContainer
CellCounts | Compute Number of Cells Positive for Certain Cytokine Combinations
checkCOMPASSConvergence | Check the convergence of multiple COMPASS models fit with different seeds.
Combinations | Generate Combinations
COMPASS | Fit the COMPASS Model
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
COMPASSDescription<- | Get and Set the Description for the Shiny Application
COMPASSfitToCountsTable | Extract a table of counts from a COMPASSResult object
COMPASSMCMCDiagnosis | Diagnostic of a set of COMPASS Models.
COMPASSResult-accessors | COMPASSResult Accessors
COMPASSResult-data | Simulated COMPASS fit
CR | Simulated COMPASS fit
FunctionalityScore | Compute the Functionality Score for each subject fit in a COMPASS model
FunctionalityScore.COMPASSResult | Compute the Functionality Score for each subject fit in a COMPASS model
FunctionalityScore.default | Compute the Functionality Score for each subject fit in a COMPASS model
Gamma | COMPASSResult Accessors
getCounts | Get a data.table of counts of polyfunctional subsets
GetThresholdedIntensities | Extract Thresholded Intensities from a GatingSet
markers | Markers
MeanGamma | COMPASSResult Accessors
melt_ | Make a 'Wide' data set 'Long'
melt_.data.frame | Make a 'Wide' data set 'Long'
melt_.matrix | Make a 'Wide' data set 'Long'
merge.COMPASSContainer | Merge Two COMPASSContainers
metadata | Metadata
metadata.COMPASSContainer | Metadata
metadata.COMPASSResult | Metadata
metadata<- | Metadata
metadata<-.COMPASSContainer | Metadata
pheatmap | A function to draw clustered heatmaps.
plot | Plot a COMPASSResult
plot.COMPASSResult | Plot a COMPASSResult
plot2 | Plot a pair of COMPASSResults
plotCOMPASSResultStack | Plot multiple COMPASSResults
PolyfunctionalityScore | Compute the Polyfunctionality Score for each subject fit in a COMPASS model
PolyfunctionalityScore.COMPASSResult | Compute the Polyfunctionality Score for each subject fit in a COMPASS model
PolyfunctionalityScore.default | Compute the Polyfunctionality Score for each subject fit in a COMPASS model
Posterior | Retrieve Posterior Measures from a COMPASS fit
PosteriorDiff | Retrieve Posterior Measures from a COMPASS fit
PosteriorLogDiff | Retrieve Posterior Measures from a COMPASS fit
PosteriorPs | Retrieve Posterior Measures from a COMPASS fit
PosteriorPu | Retrieve Posterior Measures from a COMPASS fit
print.COMPASSContainer | Print a COMPASSContainer Object
print.COMPASSResult | Print a COMPASSResult Object
Response | Compute a response probability from COMPASS mcmc samples.
Response.COMPASSResult | Compute a response probability from COMPASS mcmc samples.
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
SimpleCOMPASS | Fit the discrete COMPASS Model
subset.COMPASSContainer | Subset a COMPASSContainer
summary.COMPASSContainer | Summarize a COMPASSContainer Object
summary.COMPASSResult | Summarize a COMPASSResult Object
TotalCellCounts | Compute Total Cell Counts
translate_marker_names | Translate marker names to format use by COMPASS
transpose_list | Transpose a List
UniqueCombinations | Generate Unique Combinations
UniqueCombinations.COMPASSContainer | Generate Unique Combinations
UniqueCombinations.default | Generate Unique Combinations