| convert a gatingTemplate object to a data.table | as.data.table as.data.table.gatingTemplate |
| A class to represent a boolean gating method. | boolMethod-class |
| get gating method dimensions | dims,gtMethod-method |
| A class to represent a dummy gating method that does nothing but serves as reference to be refered by other population | dummyMethod-class |
| robust linear model using an M estimator | fast_rlm |
| constuctor for 'fcEllipsoidGate' | fcEllipsoidGate |
| a concrete class that reprents the ellipsoidGate generated by flowClust | fcEllipsoidGate-class |
| a virtual class that represents the gating result generated by flowClust gating function | fcFilter-class |
| constuctor for 'fcFilterList' | fcFilterList |
| a class that extends 'filterList' class. | fcFilterList-class |
| constuctor for 'fcPolygonGate' | fcPolygonGate |
| a concrete class that reprents the polygonGate generated by flowClust | fcPolygonGate-class |
| constuctor for 'fcRectangleGate' | fcRectangleGate |
| a concrete class that reprents the rectangleGate generated by flowClust | fcRectangleGate-class |
| constructor of 'fcTree' | fcTree |
| A class to represent a flowClust tree. | fcTree-class |
| Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters. | flowClust.1d gate_flowClust_1d gate_flowclust_1d |
| Automatic identification of a population of interest via flowClust based on two markers | flowClust.2d gate_flowClust_2d gate_flowclust_2d |
| Determines a cutpoint as the minimum point of a kernel density estimate between two peaks | gate_mindensity mindensity |
| An improved version of mindensity used to determines a cutpoint as the minimum point of a kernel density estimate between two peaks. | gate_mindensity2 mindensity2 |
| sequential quadrant gating function | gate_quad_sequential quadGate.seq |
| quadGate based on flowClust::tmixFiler | gate_quad_tmix quadGate.tmix |
| Determine the cutpoint by the events quantile. | gate_quantile quantileGate |
| Creates a singlet polygon gate using the prediction bands from a robust linear model | gate_singlet |
| a class storing the gating method and population information in a graphNEL object | gatingTemplate gatingTemplate,character-method gatingTemplate,data.table-method gatingTemplate-class |
| get gates saved in 'fcTree' | getGate,fcTree,character-method |
| get nodes from 'fcTree' | getNodes,fcTree-method |
| generate a partially complete csv template from the existing gating hierarchy | gh_generate_template templateGen |
| get the grouping variable for the gating method | groupBy,gtMethod-method |
| apply a gating method to the 'GatingSet' | add_pop gs_add_gating_method |
| Clear history of 'gs_add_gating_method' calls for a given 'GatingSet' or 'GatingSetList' | add_pop_init gs_add_gating_method_init |
| Reverse the action of gating methods applied via 'gs_add_gating_method' | gs_remove_gating_method remove_pop |
| Applies a gatingTemplate to a GatingSet. | gating gating,gatingTemplate,GatingSet-method gt_gating gt_gating,gatingTemplate,GatingSet-method gt_gating.gatingTemplate |
| get children nodes | getChildren getChildren,gatingTemplate,character-method gt_get_children |
| get gating method from the node | getGate,gatingTemplate,character-method gt_get_gate |
| get nodes from gatingTemplate object | getNodes getNodes,gatingTemplate-method gt_get_nodes |
| get parent nodes | getParent getParent,gatingTemplate,character-method gt_get_parent |
| Print a list of the registered gating methods | gt_list_methods listgtMethods |
| toggle/delete the hidden flag of the helper gates | delete.helperGates get.helperGates gt_delete_helpergates gt_get_helpergates gt_toggle_helpergates toggle.helperGates |
| A class to represent a gating method. | gtMethod gtMethod-class |
| A class to represent a cell population that will be generated by a gating method. | gtPopulation-class |
| A class representing a group of cell populations. | gtSubsets-class |
| get the flag that determines whether gating method is applied on collapsed data | isCollapse,gtMethod-method |
| get gating method name | names,gtMethod-method |
| get population name | names,gtPopulation-method |
| the class that carries event indices as well | ocRectangleGate-class |
| constructor for ocRectRefGate | ocRectRefGate |
| special gate type that mix the rectangleGate with boolean gate | ocRectRefGate-class |
| Hierarchical Gating Pipeline for flow cytometry data | openCyto |
| Deprecated functions in package 'openCyto'. | openCyto-deprecated |
| Some global options for openCyto See examples for the meaning of these options and how to get/set them. | openCyto.options |
| get parameters of the gating method/function | parameters,gtMethod-method |
| plot a 'fcFilterList' | plot,fcFilterList,ANY-method |
| plot the flowClust gating results | plot,fcTree,character-method |
| plot the gating scheme | plot,gatingTemplate,ANY-method plot,gatingTemplate,character-method plot,gatingTemplate,missing-method plot,gatingTemplate-method |
| A class to represent a polyFunctions gating method. | polyFunctions-class |
| bypass the default flowWorkspace:::.addGate | pop_add.ocRectangleGate pop_add.ocRectRefGate |
| get posteriors from a 'fcFilter' object | posteriors,fcFilter,ANY-method posteriors,fcFilter,character-method |
| A class to represent a preprocessing method. | ppMethod ppMethod-class |
| get preprocessing method from the node | ppMethod,gatingTemplate,character-method |
| apply a ppMethod to the 'GatingSet' | preprocessing,ppMethod,GatingSet-method |
| Elicits data-driven priors from a flowSet object for specified channels | prior_flowClust prior_flowclust |
| get priors from a 'fcFilter' object | priors,fcFilter,ANY-method priors,fcFilter,character-method |
| A class to represent a reference gating method. | refGate-class |
| Register a gating or preprocessing function with OpenCyto | registerGatingFunction registerPlugins register_plugins |
| rewrite huber estimator | robust_m_estimator |
| show method for boolMethod | show,boolMethod-method |
| show method for fcFilter | show,fcFilter-method |
| show method for gatingTemplate | show,gatingTemplate-method |
| show method for gtMethod | show,gtMethod-method |
