Man pages for openCyto
Hierarchical Gating Pipeline for flow cytometry data
| add | bypass the default flowWorkspace:::.addGate |
| as.data.table | convert a gatingTemplate object to a data.table |
| boolMethod-class | A class to represent a boolean gating method. |
| CytoExploreR_exports | CytoExploreR exports |
| dims-gtMethod-method | get gating method dimensions |
| dummyMethod-class | A class to represent a dummy gating method that does nothing... |
| fcEllipsoidGate | constuctor for 'fcEllipsoidGate' |
| fcEllipsoidGate-class | a concrete class that reprents the ellipsoidGate generated by... |
| fcFilter-class | a virtual class that represents the gating result generated... |
| fcFilterList | constuctor for 'fcFilterList' |
| fcFilterList-class | a class that extends 'filterList' class. |
| fcPolygonGate | constuctor for 'fcPolygonGate' |
| fcPolygonGate-class | a concrete class that reprents the polygonGate generated by... |
| fcRectangleGate | constuctor for 'fcRectangleGate' |
| fcRectangleGate-class | a concrete class that reprents the rectangleGate generated by... |
| fcTree | constructor of 'fcTree' |
| fcTree-class | A class to represent a flowClust tree. |
| gate_flowclust_1d | Applies flowClust to 1 feature to determine a cutpoint... |
| gate_flowclust_2d | Automatic identification of a population of interest via... |
| gate_mindensity | Determines a cutpoint as the minimum point of a kernel... |
| gate_mindensity2 | An improved version of mindensity used to determines a... |
| gate_quad_sequential | sequential quadrant gating function |
| gate_quad_tmix | quadGate based on flowClust::tmixFiler |
| gate_quantile | Determine the cutpoint by the events quantile. |
| gate_tail | Gates the tail of a density using the derivative of a kernel... |
| gate_tautstring | Taut String Density Estimator Gating |
| gatingTemplate-class | a class storing the gating method and population information... |
| getGate-fcTree-character-method | get gates saved in 'fcTree' |
| getNodes-fcTree-method | get nodes from 'fcTree' |
| gh_generate_template | generate a partially complete csv template from the existing... |
| groupBy-gtMethod-method | get the grouping variable for the gating method |
| gs_add_gating_method | apply a gating method to the 'GatingSet' |
| gs_add_gating_method_init | Clear history of 'gs_add_gating_method' calls for a given... |
| gs_remove_gating_method | Reverse the action of gating methods applied via... |
| gt_gating | Applies a gatingTemplate to a GatingSet. |
| gt_get_children | get children nodes |
| gt_get_gate | get gating method from the node |
| gt_get_nodes | get nodes from gatingTemplate object |
| gt_get_parent | get parent nodes |
| gt_list_methods | Print a list of the registered gating methods |
| gtMethod-class | A class to represent a gating method. |
| gtPopulation-class | A class to represent a cell population that will be generated... |
| gtSubsets-class | A class representing a group of cell populations. |
| gt_toggle_helpergates | toggle/delete the hidden flag of the helper gates |
| isCollapse-gtMethod-method | get the flag that determines whether gating method is applied... |
| names-gtMethod-method | get gating method name |
| names-gtPopulation-method | get population name |
| ocRectangleGate-class | the class that carries event indices as well |
| ocRectRefGate | constructor for ocRectRefGate |
| ocRectRefGate-class | special gate type that mix the rectangleGate with boolean... |
| openCyto | Hierarchical Gating Pipeline for flow cytometry data |
| openCyto-deprecated | Deprecated functions in package 'openCyto'. |
| openCyto.options | Some global options for openCyto See examples for the meaning... |
| parameters-gtMethod-method | get parameters of the gating method/function |
| plot-fcFilterList-ANY-method | plot a 'fcFilterList' |
| plot-fcTree-character-method | plot the flowClust gating results |
| plot-gatingTemplate-missing-method | plot the gating scheme |
| polyFunctions-class | A class to represent a polyFunctions gating method. |
| posteriors-fcFilter-ANY-method | get posteriors from a 'fcFilter' object |
| ppMethod-class | A class to represent a preprocessing method. |
| ppMethod-gatingTemplate-character-method | get preprocessing method from the node |
| preprocessing-ppMethod-GatingSet-method | apply a ppMethod to the 'GatingSet' |
| prior_flowclust | Elicits data-driven priors from a flowSet object for... |
| priors-fcFilter-ANY-method | get priors from a 'fcFilter' object |
| refGate-class | A class to represent a reference gating method. |
| register_plugins | Register a gating or preprocessing function with OpenCyto |
| show-boolMethod-method | show method for boolMethod |
| show-fcFilter-method | show method for fcFilter |
| show-gatingTemplate-method | show method for gatingTemplate |
| show-gtMethod-method | show method for gtMethod |
