Hierarchical Gating Pipeline for flow cytometry data

Documentation for package ‘openCyto’ version 2.12.0

Help Pages

-- 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.

-- 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 --

fast_rlm	robust linear model using an M estimator
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_singlet	Creates a singlet polygon gate using the prediction bands from a robust linear model
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'
robust_m_estimator	rewrite huber estimator

-- 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 --

templateGen	generate a partially complete csv template from the existing gating hierarchy
toggle.helperGates	toggle/delete the hidden flag of the helper gates