A GatingML Interface for Cross Platform Cytometry Data Sharing
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Documentation for package ‘CytoML’ version 2.21.0
Help Pages
| addCustomInfo | add customInfo nodes to each gate node and add BooleanAndGates |
| ce_get_channels | Extract channels from cytobank_experiment |
| ce_get_compensations | Obtain the spillover matrices for the samples in a Cytobank experiment |
| ce_get_markers | Extract markers from cytobank_experiment |
| ce_get_panels | Obtain counts of the number of samples associated with each marker panel in a Cytobank experiment |
| ce_get_samples | Obtain a mapping between the samples and marker panels in a Cytobank experiment |
| ce_get_transformations | Obtain the transformations associated with each channel in a Cytobank experiment |
| colnames-method | Methods for interacting with cytobank_experiment objects |
| 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 parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSet |
| cytobankExperiment | Construct a 'cytobank_experiment' object from ACS file |
| cytobank_experiment-methods | Methods for interacting with cytobank_experiment objects |
| cytobank_to_gatingset | A wrapper that parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSet |
| cytobank_to_gatingset.cytobank_experiment | A wrapper that parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSet |
| cytobank_to_gatingset.default | A wrapper that parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSet |
| CytoML-deprecated | Deprecated functions in package 'CytoML'. |
| diva_get_samples | Get a table of samples from a FACSDiva workspace |
| diva_get_sample_groups | Get a table of samples from a FACSDiva workspace |
| diva_to_gatingset | Parse a FACSDiva Workspace |
| diva_workspace-class | An R representation of a BD FACSDiva workspace |
| 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. |
| fj_ws_get_keywords | Get Keywords |
| fj_ws_get_samples | Get a list of samples from a flowJo workspace |
| fj_ws_get_sample_groups | Get a table of sample groups from a flowJo workspace |
| flowjo_to_gatingset | Parse a flowJo Workspace |
| flowjo_workspace-class | An R representation of a flowJo workspace. |
| GatingSet2cytobank | Convert a GatingSet to a Cytobank-compatible gatingML |
| GatingSet2flowJo | Convert a GatingSet to flowJo workspace |
| gatingset_to_cytobank | Convert a GatingSet to a Cytobank-compatible gatingML |
| gatingset_to_flowjo | Convert a GatingSet to flowJo workspace |
| getChildren-method | get children nodes |
| getCompensationMatrices.graphGML | Extract compensation from graphGML object. |
| getGate-method | get gate from the node |
| getKeywords | 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 |
| getSamples | Get a list of samples from a flowJo workspace |
| getTransformations.graphGML | Extract transformations from graphGML object. |
| graphGML-class | A graph object returned by 'read.gatingML.cytobank' function. |
| gs_compare_cytobank_counts | compare the counts to cytobank's exported csv so that the parsing result can be verified. |
| markernames-method | Methods for interacting with cytobank_experiment objects |
| 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 |
| open_cytobank_experiment | Construct a 'cytobank_experiment' object from ACS file |
| open_diva_xml | open Diva xml workspace |
| open_flowjo_xml | Open/Close a flowJo workspace |
| parse.gateInfo | Parse the cytobank custom_info for each gate |
| parseWorkspace | Parse a flowJo Workspace |
| parseWorkspace-method | Parse a FACSDiva Workspace |
| parseWorkspace-method | Parse a flowJo Workspace |
| pData-method | Methods for interacting with cytobank_experiment objects |
| plot-method | plot the population tree stored in graphGML. |
| print.cytobank_experiment | Methods for interacting with cytobank_experiment objects |
| range.GatingHierarchy | the parameter range from the flow data associated with GatingHierarchy |
| read.gatingML.cytobank | Parser for gatingML exported by Cytobank |
| sampleNames-method | Methods for interacting with cytobank_experiment objects |
| show-method | An R representation of a BD FACSDiva workspace |
| show-method | An R representation of a flowJo workspace. |
| show-method | show method for graphGML |