Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore

Documentation for package ‘flowWorkspace’ version 1.2.0

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C E F G H I K L O P R S misc

flowWorkspace-package

Import and replicate flowJo workspaces and gating schemes using flowCore.

-- C --

closeWorkspace	Close a flowJoWorkspace
closeWorkspace-method	Close a flowJoWorkspace
closeWorkspace-methods	Close a flowJoWorkspace

-- E --

ellipsoidGate2FlowJoVertices	Get the vertices of an ellipsoid gate needed to export it to flowJo
ellipsoidGate2FlowJoVertices-method	Get the vertices of an ellipsoid gate needed to export it to flowJo
ellipsoidGate2FlowJoVertices-methods	Get the vertices of an ellipsoid gate needed to export it to flowJo
execute	Apply the GatingHierarchy to data, computing population statistics along the way.
execute-method	Apply the GatingHierarchy to data, computing population statistics along the way.
execute-methods	Apply the GatingHierarchy to data, computing population statistics along the way.
exportAsFlowJoXML	Export a workFlow to FlowJo XML
exportAsFlowJoXML-method	Export a workFlow to FlowJo XML
exportAsFlowJoXML-methods	Export a workFlow to FlowJo XML
ExportTSVAnalysis	Export a GatingSet as a set of TSV (tab separated value) files for statistics, gates, and plots.

-- F --

flowJoWorkspace-class	Class '"flowJoWorkspace"'
flowWorkspace	Import and replicate flowJo workspaces and gating schemes using flowCore.
flowWorkspace2flowCore	Convert the GatingHierarchies in a GatingSet to a flowCore workflow.
flowWorkspace2flowCore-method	Convert the GatingHierarchies in a GatingSet to a flowCore workflow.
flowWorkspace2flowCore-methods	Convert the GatingHierarchies in a GatingSet to a flowCore workflow.

-- G --

GatingHierarchy-class	Class '"GatingHierarchy"'
GatingSet-class	Class '"GatingSet"'
getBoundaries	Get the boundaries of a flowJo gate
getBoundaries-method	Get the boundaries of a flowJo gate
getBoundaries-methods	Get the boundaries of a flowJo gate
getChildren	Returns a list of child populations of the current node in the 'GatingHierarchy'
getChildren-method	Returns a list of child populations of the current node in the 'GatingHierarchy'
getChildren-methods	Returns a list of child populations of the current node in the 'GatingHierarchy'
getCompensationMatrices	Retrieve the compensation matrices from a flowJo Workspace
getCompensationMatrices-method	Retrieve the compensation matrices from a flowJo Workspace
getCompensationMatrices-methods	Retrieve the compensation matrices from a flowJo Workspace
getData	Return the flowFrame associated with a GatingHierarchy
getData-method	Return the flowFrame associated with a GatingHierarchy
getData-methods	Return the flowFrame associated with a GatingHierarchy
getDimensions	Return the dimensions on which a gate is applied within a GatingHierarchy
getDimensions-method	Return the dimensions on which a gate is applied within a GatingHierarchy
getDimensions-methods	Return the dimensions on which a gate is applied within a GatingHierarchy
getFJWSubsetIndices	Fetch the indices for a subset of samples in a flowJo workspace, based on a keyword value pair
getGate	Return the flowCore gate definition associated with a node in a GatingHierarchy.
getGate-method	Return the flowCore gate definition associated with a node in a GatingHierarchy.
getIndiceFile	Returns the .nc file used to store the gating indices for the GatingHierarchy
getIndiceFile-method	Returns the .nc file used to store the gating indices for the GatingHierarchy
getIndiceFile-methods	Returns the .nc file used to store the gating indices for the GatingHierarchy
getIndices	Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getIndices-method	Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getIndices-methods	Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getKeywords	Get List of Keywords for a Flow Sample
getKeywords-method	Get List of Keywords for a Flow Sample
getKeywords-methods	Get List of Keywords for a Flow Sample
getNcdf	Return the ncdfFlow object storing the data
getNcdf-method	Return the ncdfFlow object storing the data
getNodes	Get the names of all nodes in a gating hierarchy
getNodes-method	Get the names of all nodes in a gating hierarchy
getNodes-methods	Get the names of all nodes in a gating hierarchy
getParent	Return the name of the parent population of the current population in the GatingHierarchy
getParent-method	Return the name of the parent population of the current population in the GatingHierarchy
getParent-methods	Return the name of the parent population of the current population in the GatingHierarchy
getPopStats	Return a table of population statistics for all populations in a GatingHierarchy
getPopStats-method	Return a table of population statistics for all populations in a GatingHierarchy
getPopStats-methods	Return a table of population statistics for all populations in a GatingHierarchy
getProp	Get the population proportions of a node (population) in a GatingHierarchy
getProp-method	Get the population proportions of a node (population) in a GatingHierarchy
getProp-methods	Get the population proportions of a node (population) in a GatingHierarchy
getSample	Get the sample name associated with a GatingHierarchy
getSample-method	Get the sample name associated with a GatingHierarchy
getSampleGroups	Get a table of sample groups from a flowJo workspace
getSampleGroups-method	Get a table of sample groups from a flowJo workspace
getSampleGroups-methods	Get a table of sample groups from a flowJo workspace
getSamples	Get a list of samples in a flowJo workspace or a GatingSet
getSamples-method	Get a list of samples in a flowJo workspace or a GatingSet
getSamples-methods	Get a list of samples in a flowJo workspace or a GatingSet
getTotal	Fetch the total number of events in a gate defined in a GatingHierarchy
getTotal-method	Fetch the total number of events in a gate defined in a GatingHierarchy
getTotal-methods	Fetch the total number of events in a gate defined in a GatingHierarchy
getTransformations	Return a list of transformations in a flowJo workspace
getTransformations-method	Return a list of transformations in a flowJo workspace
getTransformations-methods	Return a list of transformations in a flowJo workspace

-- H --

haveSameGatingHierarchy	Tests whether two GatingHierarchy or GatingSet objects have the same gating structure.
haveSameGatingHierarchy-method	Tests whether two GatingHierarchy or GatingSet objects have the same gating structure.
haveSameGatingHierarchy-methods	Tests whether two GatingHierarchy or GatingSet objects have the same gating structure.

-- I --

includedChannel2ExcludedChannel	Convert a list of parameter names in a 'GatingSet' to its complement.
includedGate2ExcludedGate	Convert a set of gates given by their flowJo gate paths to its complement (and excluding Boolean gates), referenced by gate indices recognized by 'normalizeGatingSet'.

-- K --

keyword	Methods to retrieve keywords associated with an FCS sample
keyword,GatingHierarchy,character	Methods to retrieve keywords associated with an FCS sample
keyword,GatingSet,character	Methods to retrieve keywords associated with an FCS sample
keyword-method	Methods to retrieve keywords associated with an FCS sample

-- L --

lapply-method	Methods for iterating over a gating set
lapply-methods	Methods for iterating over a gating set
length-method	Methods to get the length of a GatingSet
length-methods	Methods to get the length of a GatingSet

-- O --

openWorkspace	Open a flowJo workspace
openWorkspace-method	Open a flowJo workspace
openWorkspace-methods	Open a flowJo workspace

-- P --

parseWorkspace	Parse a flowJo Workspace
parseWorkspace-method	Parse a flowJo Workspace
parseWorkspace-methods	Parse a flowJo Workspace
plot	Plot a GatingHierarchy
plot-method	Plot a GatingHierarchy
plot-methods	Plot a GatingHierarchy
plotGate	Plot a flowJo Gate and Cell Population
plotGate-method	Plot a flowJo Gate and Cell Population
plotGate-methods	Plot a flowJo Gate and Cell Population
plotPopCV	Plot the coefficient of variation between flowJo and flowCore population statistics for each population in a gating hierarchy.
plotPopCV-method	Plot the coefficient of variation between flowJo and flowCore population statistics for each population in a gating hierarchy.
plotPopCV-methods	Plot the coefficient of variation between flowJo and flowCore population statistics for each population in a gating hierarchy.
plotWf	plot a workflow

-- R --

recomputeGatingSet

Recalculates all the gating in the GatingSet if netCDF storage is used.

-- S --

saveNcdf	Save the netcdf file of a GatingSet or GatingHierarchy to a permanent location.
show-method	Summarize a flowJoWorkspace object
show-methods	Summarize a flowJoWorkspace object
summary-method	Summarize a flowJoWorkspace object
summary-methods	Summarize a flowJoWorkspace object

-- misc --

.includedChannel2ExcludedChannel	Convert a list of parameter names in a 'GatingSet' to its complement.
.includedGate2ExcludedGate	Convert a set of gates given by their flowJo gate paths to its complement (and excluding Boolean gates), referenced by gate indices recognized by 'normalizeGatingSet'.
[-method	Class '"GatingSet"'
[[-method	Class '"GatingSet"'