Man pages for openCyto
Hierarchical Gating Pipeline for flow cytometry data

addbypass the default flowWorkspace:::.addGate
add_popapply a gating method to the 'GatingSet' a gatingTemplate object to a data.table
boolMethod-classA class to represent a boolean gating method.
dims-gtMethod-methodget gating method dimensions
dummyMethod-classA class to represent a dummy gating method that does nothing...
fcEllipsoidGateconstuctor for 'fcEllipsoidGate'
fcEllipsoidGate-classa concrete class that reprents the ellipsoidGate generated by...
fcFilter-classa virtual class that represents the gating result generated...
fcFilterListconstuctor for 'fcFilterList'
fcFilterList-classa class that extends 'filterList' class.
fcPolygonGateconstuctor for 'fcPolygonGate'
fcPolygonGate-classa concrete class that reprents the polygonGate generated by...
fcRectangleGateconstuctor for 'fcRectangleGate'
fcRectangleGate-classa concrete class that reprents the rectangleGate generated by...
fcTreeconstructor of 'fcTree'
fcTree-classA class to represent a flowClust tree.
flowClust1dApplies flowClust to 1 feature to determine a cutpoint...
flowClust2dAutomatic identification of a population of interest via...
gate_mindensityDetermines a cutpoint as the minimum point of a kernel...
gate_mindensity2An improved version of mindensity used to determines a...
gate_quad_sequentialsequential quadrant gating function
gate_quad_tmixquadGate based on flowClust::tmixFiler
gate_quantileDetermine the cutpoint by the events quantile.
gate_tailGates the tail of a density using the derivative of a kernel...
gating-gtMethod-GatingSet-methodapply a gtMethod to the 'GatingSet'
gating-methodsApply the gates to a GatingSet
gatingTemplate-classa class storing the gating method and population information...
getChildren-gatingTemplate-character-methodget children nodes
getGate-fcTree-character-methodget gates saved in 'fcTree'
getGate-gatingTemplate-character-methodget gating method from the node
getNodesget nodes from gatingTemplate object
getNodes-fcTree-methodget nodes from 'fcTree'
getParent-gatingTemplate-character-methodget parent nodes
groupBy-gtMethod-methodget the grouping variable for the gating method
gtMethod-classA class to represent a gating method.
gtPopulation-classA class to represent a cell population that will be generated...
gtSubsets-classA class representing a group of cell populations.
isCollapse-gtMethod-methodget the flag that determines whether gating method is applied...
isPolyfunctionalA function to tell wether a gating method is 'polyFunctions'
listgtMethodsPrint a list of the registered gating methods
names-gtMethod-methodget gating method name
names-gtPopulation-methodget population name
ocRectangleGate-classthe class that carries event indices as well
ocRectRefGateconstructor for ocRectRefGate
ocRectRefGate-classspecial gate type that mix the rectangleGate with boolean...
openCytoHierarchical Gating Pipeline for flow cytometry data
openCyto.optionsSome global options for openCyto See examples for the meaning...
parameters-gtMethod-methodget parameters of the gating method/function
plot-fcFilterList-ANY-methodplot a 'fcFilterList'
plot-fcTree-character-methodplot the flowClust gating results
plot-gatingTemplate-missing-methodplot the gating scheme
polyFunctions-classA class to represent a polyFunctions gating method.
posteriors-fcFilter-ANY-methodget posteriors from a 'fcFilter' object
ppMethod-classA class to represent a preprocessing method.
ppMethod-gatingTemplate-character-methodget preprocessing method from the node
preprocessing-ppMethod-GatingSet-methodapply a ppMethod to the 'GatingSet'
prior_flowClustElicits data-driven priors from a flowSet object for...
prior_flowClust1dElicits data-driven priors from a flowSet object for a...
prior_kmeansElicits data-driven priors from a flowSet object for...
priors-fcFilter-ANY-methodget priors from a 'fcFilter' object
refGate-classA class to represent a reference gating method.
registerPluginsRegister a gating or preprocessing function with OpenCyto
show-boolMethod-methodshow method for boolMethod
show-fcFilter-methodshow method for fcFilter
show-gatingTemplate-methodshow method for gatingTemplate
show-gtMethod-methodshow method for gtMethod
templateGengenerate a partially complete csv template from the existing...
toggle.helperGatestoggle/delete the hidden flag of the helper gates
openCyto documentation built on Nov. 17, 2017, 12:43 p.m.