Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore


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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"'