COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells
Version 1.14.0

COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

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AuthorLynn Lin, Kevin Ushey, Greg Finak, Ravio Kolde (pheatmap)
Bioconductor views FlowCytometry
Date of publicationNone
MaintainerGreg Finak <gfinak@fhcrc.org>
LicenseArtistic-2.0
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("COMPASS")

Man pages

categories: Categories
CellCounts: Compute Number of Cells Positive for Certain Cytokine...
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
COMPASS-package: COMPASS (Combinatorial Polyfunctionality Analysis of...
COMPASSResult-accessors: COMPASSResult Accessors
COMPASSResult-data: Simulated COMPASS fit
FunctionalityScore: Compute the Functionality Score for each subject fit in a...
getCounts: Get a data.table of counts of polyfunctional subsets
GetThresholdedIntensities: Extract Thresholded Intensities from a GatingSet
markers: Markers
melt_: Make a 'Wide' data set 'Long'
merge.COMPASSContainer: Merge Two COMPASSContainers
metadata: Metadata
pheatmap: A function to draw clustered heatmaps.
plot2: Plot a pair of COMPASSResults
plot.COMPASSResult: Plot a COMPASSResult
PolyfunctionalityScore: Compute the Polyfunctionality Score for each subject fit in a...
Posterior: Retrieve Posterior Measures from a COMPASS fit
print.COMPASSContainer: Print a COMPASSContainer Object
print.COMPASSResult: Print a COMPASSResult Object
scores: Fetch the table of scores and metadata from a COMPASSResult...
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

Functions

CC Man page
COMPASS Man page Source code
COMPASS-package Man page
COMPASS.discrete Source code
COMPASSContainer Man page Source code
COMPASSContainer-data Man page
COMPASSContainerFromGatingSet Man page Source code
COMPASSDescription Man page Source code
COMPASSDescription<- Man page
COMPASSResult-accessors Man page
COMPASSResult-data Man page
CR Man page
CellCounts Man page Source code
CellCounts.COMPASSContainer Source code
CellCounts.default Source code
CellCounts_character Source code
CellCounts_numeric Source code
Combinations Man page Source code
FunctionalityScore Man page Source code
FunctionalityScore.COMPASSResult Man page Source code
FunctionalityScore.default Man page Source code
Gamma Man page Source code
GetThresholdedIntensities Man page Source code
MakeComparable Source code
MakeComparableTwoCOMPASSResults Source code
MeanGamma Man page Source code
PolyfunctionalityScore Man page Source code
PolyfunctionalityScore.COMPASSResult Man page Source code
PolyfunctionalityScore.default Man page Source code
Posterior Man page Source code
PosteriorDiff Man page Source code
PosteriorLogDiff Man page Source code
PosteriorPs Man page Source code
PosteriorPu Man page Source code
SimpleCOMPASS Man page Source code
TotalCellCounts Man page Source code
UniqueCombinations Man page Source code
UniqueCombinations.COMPASSContainer Man page Source code
UniqueCombinations.default Man page Source code
categories Man page Source code
check_meta Source code
clamp Source code
cleanup Source code
cluster_mat Source code
compute_posterior Source code
convert_annotations Source code
convert_cytokine_annotations Source code
draw_annotation_legend Source code
draw_annotations Source code
draw_colnames Source code
draw_dendrogram Source code
draw_headerplot Source code
draw_legend Source code
draw_main Source code
draw_matrix Source code
draw_polar_legend Source code
draw_row_annotations Source code
draw_rownames Source code
generate_annotation_colours Source code
generate_breaks Source code
generate_row_annotation_colours Source code
getCounts Man page Source code
heatmap_motor Source code
kmeans_pheatmap Source code
lo Source code
markers Man page Source code
markers.COMPASSContainer Source code
markers.COMPASSResult Source code
melt_ Man page Source code
melt_.data.frame Man page Source code
melt_.matrix Man page Source code
merge.COMPASSContainer Man page Source code
metadata Man page Source code
metadata.COMPASSContainer Man page Source code
metadata.COMPASSResult Man page Source code
metadata<- Man page
metadata<-.COMPASSContainer Man page
needsFlowWorkspace Source code
onLoad Source code
pheatmap Man page Source code
plot Man page
plot.COMPASSResult Man page Source code
plot2 Man page Source code
polarLegend Source code
print.COMPASSContainer Man page Source code
print.COMPASSResult Man page Source code
sBoolGate Source code
scale_colours Source code
scale_mat Source code
scale_rows Source code
scale_vec_colours Source code
scores Man page Source code
select_compass_pops Man page Source code
shinyCOMPASS Man page Source code
shinyCOMPASSDeps Man page Source code
stopf Source code
subset.COMPASSContainer Man page Source code
summary.COMPASSContainer Man page Source code
summary.COMPASSResult Man page Source code
swap Source code
toCart Source code
translate_marker_names Man page Source code
transpose_list Man page Source code
vplayout Source code
warnf Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/COMPASS-data.R
R/COMPASS-discrete.R
R/COMPASS-package.R
R/COMPASS.R
R/COMPASSContainer.R
R/COMPASSResult-methods.R
R/CellCounts.R
R/Combinations.R
R/GatingSetToCOMPASS.R
R/GetThresholdedIntensities.R
R/Posterior.R
R/RcppExports.R
R/Scores.R
R/SimpleCOMPASS.R
R/TotalCounts.R
R/UniqueCombinations.R
R/check_meta.R
R/cleanup.R
R/commonPlot.R
R/description.R
R/melt_.R
R/merge-COMPASSContainer.R
R/miscellaneous.R
R/pheatmap.R
R/plotMeanGamma-2.R
R/plotMeanGamma.R
R/shinyCOMPASS.R
R/shinyCOMPASSDeps.R
R/subset-COMPASSContainer.R
R/swap.R
R/transpose_list.R
R/utils.R
R/zzz.R
README.md
build
build/vignette.rds
cleanup
data
data/COMPASS.rda
examples
incubator
inst
inst/doc
inst/doc/COMPASS.R
inst/doc/COMPASS.Rmd
inst/doc/COMPASS.html
inst/shiny
inst/shiny/common_functions.R
inst/shiny/scripts.js
inst/shiny/server.R
inst/shiny/ui.R
inst/shiny/withHelp.R
inst/shiny/www
inst/shiny/www/css
inst/shiny/www/css/shinySplom.css
inst/shiny/www/css/styles.css
inst/shiny/www/jquery-ui
inst/shiny/www/jquery-ui/css
inst/shiny/www/jquery-ui/css/ui-lightness
inst/shiny/www/jquery-ui/css/ui-lightness/images
inst/shiny/www/jquery-ui/css/ui-lightness/images/animated-overlay.gif
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_222222_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_228ef1_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ef8c08_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ffd27a_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/images/ui-icons_ffffff_256x240.png
inst/shiny/www/jquery-ui/css/ui-lightness/jquery-ui-1.10.3.custom.css
inst/shiny/www/jquery-ui/css/ui-lightness/jquery-ui-1.10.3.custom.min.css
inst/shiny/www/jquery-ui/js
inst/shiny/www/jquery-ui/js/jquery-1.9.1.js
inst/shiny/www/jquery-ui/js/jquery-ui-1.10.3.custom.js
inst/shiny/www/jquery-ui/js/jquery-ui-1.10.3.custom.min.js
inst/shiny/www/js
inst/shiny/www/js/d3.js
inst/shiny/www/js/fancyboxify.js
inst/shiny/www/js/gridsterExtras.js
inst/shiny/www/js/resize.js
inst/shiny/www/js/shinySplom.js
inst/shiny/www/js/tooltips.js
inst/shiny/www/js/updateSubsets.js
inst/shiny/www/multiselect
inst/shiny/www/multiselect/multiselect.css
inst/shiny/www/multiselect/multiselect.js
inst/shiny/www/opentip
inst/shiny/www/opentip/opentip.css
inst/shiny/www/opentip/opentip.js
internal
man
man/COMPASS-package.Rd
man/COMPASS.Rd
man/COMPASSContainer-data.Rd
man/COMPASSContainer.Rd
man/COMPASSContainerFromGatingSet.Rd
man/COMPASSDescription.Rd
man/COMPASSResult-accessors.Rd
man/COMPASSResult-data.Rd
man/CellCounts.Rd
man/Combinations.Rd
man/FunctionalityScore.Rd
man/GetThresholdedIntensities.Rd
man/PolyfunctionalityScore.Rd
man/Posterior.Rd
man/SimpleCOMPASS.Rd
man/TotalCellCounts.Rd
man/UniqueCombinations.Rd
man/categories.Rd
man/getCounts.Rd
man/markers.Rd
man/melt_.Rd
man/merge.COMPASSContainer.Rd
man/metadata.Rd
man/pheatmap.Rd
man/plot.COMPASSResult.Rd
man/plot2.Rd
man/print.COMPASSContainer.Rd
man/print.COMPASSResult.Rd
man/scores.Rd
man/select_compass_pops.Rd
man/shinyCOMPASS.Rd
man/shinyCOMPASSDeps.Rd
man/subset.COMPASSContainer.Rd
man/summary.COMPASSContainer.Rd
man/summary.COMPASSResult.Rd
man/translate_marker_names.Rd
man/transpose_list.Rd
refactor
scratch
src
src/COMPASS_init.c
src/CellCounts.cpp
src/CellCounts_character.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/digamma.c
src/mat2vec.c
src/melt_dataframe.c
src/melt_matrix.c
src/samplePuPs.cpp
src/transpose_list.c
src/updatealphas_Exp.cpp
src/updatealphau.cpp
src/updatealphau_noPu_Exp.cpp
src/updatebeta_RW.cpp
src/updategammak_noPu.cpp
src/utils.c
tests
tests/test-all.R
tests/testthat
tests/testthat/helper-init.R
tests/testthat/test-COMPASS.R
tests/testthat/test-CellCounts.R
tests/testthat/test-FunctionalityScore.R
tests/testthat/test-GatingSet2COMPASS.R
vignettes
vignettes/COMPASS.Rmd
COMPASS documentation built on May 20, 2017, 9:47 p.m.