Combinatorial Polyfunctionality Analysis of Single Cells


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Documentation for package ‘COMPASS’ version 1.24.1

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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