flowWorkspace-package | Import and replicate flowJo workspaces and gating schemes using flowCore. |
closeWorkspace | Close a flowJoWorkspace |
closeWorkspace-method | Close a flowJoWorkspace |
closeWorkspace-methods | Close a flowJoWorkspace |
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 |
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. |
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. |
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 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 |
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 |
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 |
openWorkspace | Open a flowJo workspace |
openWorkspace-method | Open a flowJo workspace |
openWorkspace-methods | Open a flowJo workspace |
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 |
show-method | Summarize a flowJoWorkspace object |
show-methods | Summarize a flowJoWorkspace object |
summary-method | Summarize a flowJoWorkspace object |
summary-methods | Summarize a flowJoWorkspace object |
[-method | Class '"GatingSet"' |
[<--method | Replace parts of a GatingSet |
[[-method | Class '"GatingSet"' |
[[<--method | Replace parts of a GatingSet |