| addCustomInfo | add customInfo nodes to each gate node and add BooleanAndGates |
| closeWorkspace | Open/Close a flowJo workspace |
| closeWorkspace-method | Open/Close a flowJo workspace |
| colnames-method | Construct cytobankExperiment object from ACS file |
| compare.counts | compare the counts to cytobank's exported csv so that the parsing result can be verified. |
| compensate-method | compensate a GatingSet based on the compensation information stored in graphGML object |
| constructTree | Reconstruct the population tree from the GateSets |
| cytobank2GatingSet | A wrapper that parse the gatingML and FCS files (or cytobankExperiment object) into GatingSet |
| cytobank2GatingSet.cytobankExperiment | A wrapper that parse the gatingML and FCS files (or cytobankExperiment object) into GatingSet |
| cytobank2GatingSet.default | A wrapper that parse the gatingML and FCS files (or cytobankExperiment object) into GatingSet |
| cytobankExperiment | Construct cytobankExperiment object from ACS file |
| CytoML.par.get | CytoML.par.set sets a set of parameters in the CytoML package namespace. |
| CytoML.par.init | workspace version is parsed from xml node '/Workspace/version' in flowJo workspace and matched with this list to dispatch to the one of the three workspace parsers |
| CytoML.par.set | CytoML.par.set sets a set of parameters in the CytoML package namespace. |
| divaWorkspace-class | divaWorkspace class Inherited from flowJoWorkspace-class |
| extend | extend the gate to the minimum and maximum limit of both dimensions based on the bounding information. |
| extend.ellipsoidGate | extend the gate to the minimum and maximum limit of both dimensions based on the bounding information. |
| extend.polygonGate | extend the gate to the minimum and maximum limit of both dimensions based on the bounding information. |
| extend.rectangleGate | extend the gate to the minimum and maximum limit of both dimensions based on the bounding information. |
| flowJoWorkspace-class | An R representation of a flowJo workspace. |
| gating-method | Apply the gatingML graph to a GatingSet |
| GatingSet | constructors for GatingSet |
| GatingSet-method | constructors for GatingSet |
| GatingSet2cytobank | Convert a GatingSet to a Cytobank-compatible gatingML |
| GatingSet2flowJo | Convert a GatingSet to flowJo workspace |
| getChildren-method | get children nodes |
| getCompensationMatrices | Construct cytobankExperiment object from ACS file |
| getCompensationMatrices.cytobankExperiment | Construct cytobankExperiment object from ACS file |
| getCompensationMatrices.graphGML | Extract compensation from graphGML object. |
| getFJWSubsetIndices | Fetch the indices for a subset of samples in a flowJo workspace, based on a keyword value pair |
| getGate-method | get gate from the node |
| getKeywords | Get Keywords |
| getKeywords-method | Get Keywords |
| getNodes-method | get nodes from graphGML object |
| getParent-method | get parent nodes |
| getSampleGroups | Get a table of sample groups from a flowJo workspace |
| getSampleGroups-method | divaWorkspace class Inherited from flowJoWorkspace-class |
| getSampleGroups-method | Get a table of sample groups from a flowJo workspace |
| getSamples | Get a list of samples from a flowJo workspace |
| getSamples-method | divaWorkspace class Inherited from flowJoWorkspace-class |
| getSamples-method | Get a list of samples from a flowJo workspace |
| getTransformations | Construct cytobankExperiment object from ACS file |
| getTransformations.cytobankExperiment | Construct cytobankExperiment object from ACS file |
| getTransformations.graphGML | Extract transformations from graphGML object. |
| graphGML-class | A graph object returned by 'read.gatingML.cytobank' function. |
| markernames-method | Construct cytobankExperiment object from ACS file |
| matchPath | Given the leaf node, try to find out if a collection of nodes can be matched to a path in a graph(tree) by the bottom-up searching |
| openDiva | open Diva xml workspace |
| openWorkspace | Open/Close a flowJo workspace |
| openWorkspace.character | Open/Close a flowJo workspace |
| parse.gateInfo | Parse the cytobank custom_info for each gate |
| parseWorkspace | Parse a flowJo Workspace |
| parseWorkspace-method | divaWorkspace class Inherited from flowJoWorkspace-class |
| parseWorkspace-method | Parse a flowJo Workspace |
| pData-method | Construct cytobankExperiment object from ACS file |
| plot-method | plot the population tree stored in graphGML. |
| print.cytobankExperiment | Construct cytobankExperiment object from ACS file |
| range.GatingHierarchy | the parameter range from the flow data associated with GatingHierarchy |
| read.gatingML.cytobank | Parser for gatingML exported by Cytobank |
| sampleNames-method | Construct cytobankExperiment object from ACS file |
| show-method | divaWorkspace class Inherited from flowJoWorkspace-class |
| show-method | An R representation of a flowJo workspace. |
| show-method | show method for graphGML |