A B C D F G I L M N O P Q R S T misc
| add_pop | apply a gating method to the 'GatingSet' |
| add_pop_init | Clear history of 'gs_add_gating_method' calls for a given 'GatingSet' or 'GatingSetList' |
| as.data.table | convert a gatingTemplate object to a data.table |
| as.data.table.gatingTemplate | convert a gatingTemplate object to a data.table |
| boolMethod-class | A class to represent a boolean gating method. |
| cytokine | Gates the tail of a density using the derivative of a kernel density estimate |
| delete.helperGates | toggle/delete the hidden flag of the helper gates |
| dims-method | get gating method dimensions |
| dummyMethod-class | A class to represent a dummy gating method that does nothing but serves as reference to be refered by other population |
| fcEllipsoidGate | constuctor for 'fcEllipsoidGate' |
| fcEllipsoidGate-class | a concrete class that reprents the ellipsoidGate generated by flowClust |
| fcFilter-class | a virtual class that represents the gating result generated by flowClust gating function |
| 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 flowClust |
| fcRectangleGate | constuctor for 'fcRectangleGate' |
| fcRectangleGate-class | a concrete class that reprents the rectangleGate generated by flowClust |
| fcTree | constructor of 'fcTree' |
| fcTree-class | A class to represent a flowClust tree. |
| flowClust.1d | Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters. |
| flowClust.2d | Automatic identification of a population of interest via flowClust based on two markers |
| gate_flowClust_1d | Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters. |
| gate_flowclust_1d | Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters. |
| gate_flowClust_2d | Automatic identification of a population of interest via flowClust based on two markers |
| gate_flowclust_2d | Automatic identification of a population of interest via flowClust based on two markers |
| gate_mindensity | Determines a cutpoint as the minimum point of a kernel density estimate between two peaks |
| gate_mindensity2 | An improved version of mindensity used to determines a cutpoint as the minimum point of a kernel density estimate between two peaks. |
| 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 density estimate |
| gate_tautstring | Taut String Density Estimator Gating |
| gating | Applies a gatingTemplate to a GatingSet. |
| gating-method | Applies a gatingTemplate to a GatingSet. |
| gatingTemplate | a class storing the gating method and population information in a graphNEL object |
| gatingTemplate-class | a class storing the gating method and population information in a graphNEL object |
| gatingTemplate-method | a class storing the gating method and population information in a graphNEL object |
| get.helperGates | toggle/delete the hidden flag of the helper gates |
| getChildren | get children nodes |
| getChildren-method | get children nodes |
| getGate-method | get gates saved in 'fcTree' |
| getGate-method | get gating method from the node |
| getNodes | get nodes from gatingTemplate object |
| getNodes-method | get nodes from 'fcTree' |
| getNodes-method | get nodes from gatingTemplate object |
| getParent | get parent nodes |
| getParent-method | get parent nodes |
| gh_generate_template | generate a partially complete csv template from the existing gating hierarchy |
| groupBy-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 'GatingSet' or 'GatingSetList' |
| gs_remove_gating_method | Reverse the action of gating methods applied via 'gs_add_gating_method' |
| gtMethod | A class to represent a gating method. |
| gtMethod-class | A class to represent a gating method. |
| gtPopulation-class | A class to represent a cell population that will be generated by a gating method. |
| gtSubsets-class | A class representing a group of cell populations. |
| gt_delete_helpergates | toggle/delete the hidden flag of the helper gates |
| gt_gating | Applies a gatingTemplate to a GatingSet. |
| gt_gating-method | Applies a gatingTemplate to a GatingSet. |
| gt_gating.gatingTemplate | Applies a gatingTemplate to a GatingSet. |
| gt_get_children | get children nodes |
| gt_get_gate | get gating method from the node |
| gt_get_helpergates | toggle/delete the hidden flag of the helper gates |
| 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 |
| gt_toggle_helpergates | toggle/delete the hidden flag of the helper gates |
| isCollapse-method | get the flag that determines whether gating method is applied on collapsed data |
| listgtMethods | Print a list of the registered gating methods |
| mindensity | Determines a cutpoint as the minimum point of a kernel density estimate between two peaks |
| mindensity2 | An improved version of mindensity used to determines a cutpoint as the minimum point of a kernel density estimate between two peaks. |
| names-method | get gating method name |
| names-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 gate |
| 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 of these options and how to get/set them. |
| parameters-method | get parameters of the gating method/function |
| plot-method | plot a 'fcFilterList' |
| plot-method | plot the flowClust gating results |
| plot-method | plot the gating scheme |
| polyFunctions-class | A class to represent a polyFunctions gating method. |
| pop_add.ocRectangleGate | bypass the default flowWorkspace:::.addGate |
| pop_add.ocRectRefGate | bypass the default flowWorkspace:::.addGate |
| posteriors-method | get posteriors from a 'fcFilter' object |
| ppMethod | A class to represent a preprocessing method. |
| ppMethod-class | A class to represent a preprocessing method. |
| ppMethod-method | get preprocessing method from the node |
| preprocessing-method | apply a ppMethod to the 'GatingSet' |
| priors-method | get priors from a 'fcFilter' object |
| prior_flowClust | Elicits data-driven priors from a flowSet object for specified channels |
| prior_flowclust | Elicits data-driven priors from a flowSet object for specified channels |
| quadGate.seq | sequential quadrant gating function |
| quadGate.tmix | quadGate based on flowClust::tmixFiler |
| quantileGate | Determine the cutpoint by the events quantile. |
| refGate-class | A class to represent a reference gating method. |
| registerGatingFunction | Register a gating or preprocessing function with OpenCyto |
| registerPlugins | Register a gating or preprocessing function with OpenCyto |
| register_plugins | Register a gating or preprocessing function with OpenCyto |
| remove_pop | Reverse the action of gating methods applied via 'gs_add_gating_method' |
| show-method | show method for boolMethod |
| show-method | show method for fcFilter |
| show-method | show method for gatingTemplate |
| show-method | show method for gtMethod |
| tailgate | Gates the tail of a density using the derivative of a kernel density estimate |
| tautString | Taut String Density Estimator Gating |
| tautstring | Taut String Density Estimator Gating |
| tautStringGate | Taut String Density Estimator Gating |
| templateGen | generate a partially complete csv template from the existing gating hierarchy |
| toggle.helperGates | toggle/delete the hidden flag of the helper gates |
| .cytokine_cutpoint | Gates the tail of a density using the derivative of a kernel density estimate |