A GatingML Interface for Cross Platform Cytometry Data Sharing


[Up] [Top]

Documentation for package ‘CytoML’ version 1.10.0

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