# Hierarchical Gating Pipeline for flow cytometry data

## Documentation for package ‘openCyto’ version 1.16.1

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

## Help Pages

openCyto-package | Hierarchical Gating Pipeline for flow cytometry data
.isPolyfunctional | A function to tell wether a gating method is 'polyFunctions'
.prior_flowClust1d | Elicits data-driven priors from a flowSet object for a specified channel
.prior_kmeans | Elicits data-driven priors from a flowSet object for specified channels using the K-Means clustering algorithm
add-method | bypass the default flowWorkspace:::.addGate
add_pop | apply a gating method to the 'GatingSet'
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_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
gating | Apply the gates to a GatingSet
gating-method | apply a gtMethod to the 'GatingSet'
gating-method | Apply the gates 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-method | get children nodes
getGate-method | get gates saved in 'fcTree'
getGate-method | get gating method from the node
getNodes-method | get nodes from 'fcTree'
getNodes-method | get nodes from gatingTemplate object
getParent-method | get parent nodes
groupBy-method | get the grouping variable for the 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.
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.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.
posteriors-method | get posteriors from a 'fcFilter' object
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
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
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
templateGen | generate a partially complete csv template from the existing gating hierarchy
toggle.helperGates | toggle/delete the hidden flag of the helper gates