filterObject |
convert flowCore filter to a list |
filterObject-method |
convert flowCore filter to a list |
flowData |
Fetch or replace the flowData object associated with a GatingSet . |
flowData-method |
Fetch or replace the flowData object associated with a GatingSet . |
flowData<- |
Fetch or replace the flowData object associated with a GatingSet . |
flowData<--method |
Fetch or replace the flowData object associated with a GatingSet . |
flowJo.fasinh |
inverse hyperbolic sine transform function |
flowJo.fsinh |
inverse hyperbolic sine transform function |
flowJoTrans |
construct the flowJo-type biexponentioal transformation function |
flowJoWorkspace-class |
An R representation of a flowJo workspace. |
flowJo_biexp_trans |
flowJo biexponential transformation. |
flowJo_fasinh_trans |
flowJo inverse hyperbolic sine transformation. |
flowWorkspace |
Import and replicate flowJo workspaces and gating schemes using flowCore. |
flowWorkspace.par.get |
flowWorkspace.par.set sets a set of parameters in the flowWorkspace package namespace. |
flowWorkspace.par.init |
workspace version is parsed from xml node '/Workspace/version' in flowJo workspace and matched with this list to dispatch to the one of the three workspace parsers |
flowWorkspace.par.set |
flowWorkspace.par.set sets a set of parameters in the flowWorkspace package namespace. |
flow_breaks |
Generate the breaks that makes sense for flow data visualization |
flow_trans |
helper function to generate a trans objects Used by other specific trans constructor |
GatingHierarchy-class |
Class GatingHierarchy |
GatingSet |
constructors for GatingSet |
GatingSet-class |
Class '"GatingSet"' |
GatingSet-method |
constructors for GatingSet |
GatingSetList |
Class '"GatingSetList"' |
GatingSetList-class |
Class '"GatingSetList"' |
getChildren |
Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy |
getChildren-method |
Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy |
getCompensationMatrices |
Retrieve the compensation matrices from a GatingHierarchy |
getCompensationMatrices-method |
Retrieve the compensation matrices from a GatingHierarchy |
getData |
get gated flow data from a GatingHierarchy/GatingSet/GatingSetList |
getData-method |
get gated flow data from a GatingHierarchy/GatingSet/GatingSetList |
getFJWSubsetIndices |
Fetch the indices for a subset of samples in a flowJo workspace, based on a keyword value pair |
getGate |
Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet. |
getGate-method |
Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet. |
getIndiceMat |
Return the single-cell matrix of 1/0 dichotomized expression |
getIndices |
Get the membership indices for each event with respect to a particular gate in a GatingHierarchy |
getIndices-method |
routine to return the indices by specify boolean combination of reference nodes: |
getIndices-method |
Get the membership indices for each event with respect to a particular gate in a GatingHierarchy |
getKeywords |
Get Keywords |
getKeywords-method |
Get Keywords |
getLoglevel |
get/set the log level |
getNodes |
Get the names of all nodes from a gating hierarchy. |
getNodes-method |
Get the names of all nodes from a gating hierarchy. |
getParent |
Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy |
getParent-method |
Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy |
getPopStats |
Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy |
getPopStats-method |
Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy |
getProp |
Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy |
getProp-method |
Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy |
getSampleGroups |
Get a table of sample groups from a flowJo workspace |
getSampleGroups-method |
Get a table of sample groups from a flowJo workspace |
getSamples |
Get a list of samples from a flowJo workspace |
getSamples-method |
Get a list of samples from a flowJo workspace |
getSingleCellExpression |
Return the cell events data that express in any of the single populations defined in 'y' |
getSingleCellExpression-method |
Return the cell events data that express in any of the single populations defined in 'y' |
getTotal |
Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy |
getTotal-method |
Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy |
getTransformations |
Return a list of transformations or a transformation in a GatingHierarchy |
getTransformations-method |
Return a list of transformations or a transformation in a GatingHierarchy |
groupByChannels |
split GatingSets into groups based on their flow channels |
groupByTree |
split GatingSets into groups based on their gating schemes Be careful that the splitted resluts still points to the original data set!! |
parseWorkspace |
Parse a flowJo Workspace |
parseWorkspace-method |
Parse a flowJo Workspace |
pData |
read/set pData of flow data associated with 'GatingSet' or 'GatingSetList' |
pData-method |
read/set pData of flow data associated with 'GatingSet' or 'GatingSetList' |
pData<- |
read/set pData of flow data associated with 'GatingSet' or 'GatingSetList' |
pData<--method |
read/set pData of flow data associated with 'GatingSet' or 'GatingSetList' |
plot |
plot a gating tree |
plot-method |
plot a gating tree |
plotGate |
Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet' |
plotGate-method |
Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet' |
plotGate-methods |
Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet' |
plotPopCV |
Plot the coefficient of variation between flowJo and flowCore population statistics for each population in a gating hierarchy. |
plotPopCV-method |
Plot the coefficient of variation between flowJo and flowCore population statistics for each population in a gating hierarchy. |
prettyAxis |
Determine tick mark locations and labels for a given channel axis |