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 |
alias |
get gating method name |
alias-method |
get gating method name |
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 after standardizing and collapsing flowFrames |
dims |
get gating method name |
dims-method |
get gating method name |
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 |
gating |
Applies gatingTemplate to one GatingSet. |
gating-method |
Applies gatingTemplate to one 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 |
get nodes from gatingTemplate object |
getChildren-method |
get nodes from gatingTemplate object |
getGate |
get nodes from gatingTemplate object |
getGate-method |
get nodes from gatingTemplate object |
getNodes |
get nodes from gatingTemplate object |
getNodes-method |
get nodes from gatingTemplate object |
getParent |
get nodes from gatingTemplate object |
getParent-method |
get nodes from gatingTemplate object |
groupBy |
get gating method name |
groupBy-method |
get gating method name |
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 |
get gating method name |
isCollapse-method |
get gating method name |
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 |
names |
get gating method name |
names-method |
get gating method name |
openCyto |
Hierarchical Gating Pipeline for flow cytometry data |
parameters |
get gating method name |
parameters-method |
get gating method name |
plot |
plot a 'fcFilterList' |
plot-method |
get nodes from gatingTemplate object |
polyFunctions-class |
A class to represent a polyFunctions gating method. |
posteriors |
get posteriors from a 'fcFilter' object |
posteriors-method |
get posteriors from a 'fcFilter' object |
ppMethod |
get nodes from gatingTemplate object |
ppMethod-class |
A class to represent a preprocessing method. |
ppMethod-method |
get nodes from gatingTemplate object |
preprocessing |
apply a ppMethod to the 'GatingSet' |
preprocessing-method |
apply a ppMethod to the 'GatingSet' |
priors |
get priors from a 'fcFilter' object |
priors-method |
get priors from a 'fcFilter' object |
prior_flowClust |
Elicits data-driven priors from a flowSet object for specified channels |
refGate-class |
A class to represent a reference gating method. |
registerPlugins |
Register a gating or preprocessing function with OpenCyto |
show |
a class storing the gating method and population information in a graphNEL object |
show-method |
a class storing the gating method and population information in a graphNEL object |
show-method |
A class to represent a gating method. |
tailgate |
Gates the tail of a density using the derivative of a kernel density estimate after standardizing and collapsing flowFrames |
templateGen |
generate a partially complete csv template from the existing gating hierarchy |