COMPASS-package | COMPASS (Combinatorial Polyfunctionality Analysis of Single-Cells) |
categories | Categories |
CC | Simulated COMPASSContainer |
CellCounts | Compute Number of Cells Positive for Certain Cytokine Combinations |
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 |
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 |