Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore


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Documentation for package ‘flowWorkspace’ version 1.6.1

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

flowWorkspace-package Import and replicate flowJo workspaces and gating schemes using flowCore.

-- A --

add Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
add-method Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
archive Archive/unarchive a GatingSetInternal to/from tar files

-- B --

booleanFilter Class '"booleanFilter"'
booleanFilter-class Class '"booleanFilter"'

-- C --

char2booleanFilter Class '"booleanFilter"'
clone clone a GatingSet
clone-method clone a GatingSet
clone-methods clone a GatingSet
closeWorkspace Open/Close a flowJo workspace
closeWorkspace-method Open/Close a flowJo workspace
closeWorkspace-methods Open/Close a flowJo workspace

-- 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"'
GatingHierarchyInternal-class Class '"GatingHierarchy"'
GatingSet Class '"GatingSet"'
GatingSet-class Class '"GatingSet"'
GatingSet-method Class '"GatingSet"'
GatingSetInternal-class Class '"GatingSet"'
GatingSetList Class '"GatingSetList"'
GatingSetList-class Class '"GatingSetList"'
getBoundaries Get the boundaries of a gate or dimensions on which a gate is applied within a GatingHierarchy
getBoundaries-method Get the boundaries of a gate or dimensions on which a gate is applied within a GatingHierarchy
getBoundaries-methods Get the boundaries of a gate or dimensions on which a gate is applied within a GatingHierarchy
getChildren Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getChildren-method Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getChildren-methods Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getCompensationMatrices Retrieve the compensation matrices from a flowJo Workspace or GatingHierarchy
getCompensationMatrices-method Retrieve the compensation matrices from a flowJo Workspace or GatingHierarchy
getCompensationMatrices-methods Retrieve the compensation matrices from a flowJo Workspace or GatingHierarchy
getData Return the flowFrame/flowSet associated with a GatingHierarchy/GatingSet
getData-method Return the flowFrame/flowSet associated with a GatingHierarchy/GatingSet
getData-methods Return the flowFrame/flowSet associated with a GatingHierarchy/GatingSet
getDimensions Get the boundaries of a gate or dimensions on which a gate is applied within a GatingHierarchy
getDimensions-method Get the boundaries of a gate or dimensions on which a gate is applied within a GatingHierarchy
getDimensions-methods Get the boundaries of a gate or 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/GatingSet.
getGate-method Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.
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
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 or a list of child populations of the current population in the GatingHierarchy
getParent-method Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getParent-methods Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getPopStats Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getPopStats-method Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getPopStats-methods Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getProp Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getProp-method Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getProp-methods Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events 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 Class '"GatingSetList"'
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 Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getTotal-method Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getTotal-methods Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getTransformations Return a list of transformations or a transformation in a flowJo workspace/GatingHierarchy
getTransformations-method Return a list of transformations or a transformation in a flowJo workspace/GatingHierarchy
getTransformations-methods Return a list of transformations or a transformation in a flowJo workspace/GatingHierarchy

-- 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 'normalize'.

-- K --

keyword Methods to retrieve keywords associated with an FCS sample
keyword,GatingHierarchy,character Methods to retrieve keywords associated with an FCS sample
keyword,GatingHierarchyInternal,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/Close a flowJo workspace
openWorkspace-method Open/Close a flowJo workspace
openWorkspace-methods Open/Close 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 Gate and Cell Population
plotGate-method Plot a Gate and Cell Population
plotGate-methods Plot a Gate and Cell Population
plotGate_labkey Plot a 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 --

rbind2-method Class '"GatingSet"'
rbind2-method Class '"GatingSetList"'
recompute Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
recompute-method Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
recomputeGatingSet Recalculates all the gating in the GatingSet if netCDF storage is used.
Rm Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
Rm-method Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.

-- S --

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

-- U --

unarchive Archive/unarchive a GatingSetInternal to/from tar files

-- 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 'normalize'.
[-method Class '"GatingSet"'
[[-method Class '"GatingSet"'