# A GatingML Interface for Cross Platform Cytometry Data Sharing

## Documentation for package ‘CytoML’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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