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' |
alias-method | get population alias |
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 |
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. |
filterObject-method | construct logicalGate obj |
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 |
gating-method | apply a 'boolMethod' to the 'GatingSet' |
gating-method | apply a gtMethod to the 'GatingSet' |
gating-method | Applies gatingTemplate to one GatingSet. |
gating-method | apply a 'polyFunctions' gating method to the 'GatingSet' |
gating-method | apply a 'refGate' to the '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 |
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 |
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 |
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 |