# Hierarchical Gating Pipeline for flow cytometry data

## Documentation for package ‘openCyto’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D F G I L M N O P Q R S T misc

## -- A --

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

## -- B --

boolMethod-class | A class to represent a boolean gating method.

## -- C --

cytokine | Gates the tail of a density using the derivative of a kernel density estimate

## -- D --

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

## -- F --

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

## -- G --

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

## -- I --

isCollapse-method | get the flag that determines whether gating method is applied on collapsed data

## -- L --

listgtMethods | Print a list of the registered gating methods

## -- M --

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.

## -- N --

names-method | get gating method name
names-method | get population name

## -- O --

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.

## -- P --

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

## -- Q --

quadGate.seq | sequential quadrant gating function
quadGate.tmix | quadGate based on flowClust::tmixFiler
quantileGate | Determine the cutpoint by the events quantile.

## -- R --

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'

## -- S --

show-method | show method for boolMethod
show-method | show method for fcFilter
show-method | show method for gatingTemplate
show-method | show method for gtMethod

## -- T --

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

## -- misc --

.cytokine_cutpoint | Gates the tail of a density using the derivative of a kernel density estimate