Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore

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Documentation for package ‘flowWorkspace’ version 3.8.61

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A B C F G I K L M N O P R S U misc

flowWorkspace-package Import and replicate flowJo workspaces and gating schemes using flowCore.

-- A --

add Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
add-method Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
archive archive/unarchive to/from a tar file

-- B --

booleanFilter A class describing logical operation (& or |) of the reference populations
booleanFilter-class A class describing logical operation (& or |) of the reference populations

-- C --

char2booleanFilter A class describing logical operation (& or |) of the reference populations
clone clone a GatingSet
clone-method clone a GatingSet
clone-methods clone a GatingSet
closeWorkspace Open/Close a flowJo workspace
closeWorkspace-method Open/Close a flowJo workspace
closeWorkspace-methods Open/Close a flowJo workspace

-- F --

flowData Fetch or replace the flowData object associated with a GatingSet .
flowData-method Fetch or replace the flowData object associated with a GatingSet .
flowData-methods 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 .
flowJoWorkspace-class An R representation of a flowJo workspace.
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.

-- G --

GatingHierarchy-class Class GatingHierarchy
GatingSet constructors for GatingSet
GatingSet-class Class '"GatingSet"'
GatingSet-method Class '"GatingSet"'
GatingSet-method constructors for GatingSet
GatingSetList Class '"GatingSetList"'
GatingSetList-class Class '"GatingSetList"'
GatingSetList-method get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
getChannelMarker get channel and marker information from a 'flowFrame' that matches to the given keyword
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
getChildren-methods 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
getCompensationMatrices-methods 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 Class '"GatingSetList"'
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 Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getIndices-methods Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getKeywords Get Keywords
getKeywords-method Get Keywords
getKeywords-methods Get Keywords
getNodes Get the names of all nodes in a gating hierarchy.
getNodes-method Get the names of all nodes in a gating hierarchy.
getNodes-methods Get the names of all nodes in 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
getParent-methods 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 Class '"GatingSetList"'
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
getPopStats-methods 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
getProp-methods 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
getQAStats-method Class '"GatingSetList"'
getSample Get the sample name associated with a GatingHierarchy
getSample-method Get the sample name associated with 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
getSampleGroups-methods Get a table of sample groups from a flowJo workspace
getSamples Get a list of samples from a flowJo workspace
getSamples-method Class '"GatingSetList"'
getSamples-method Get a list of samples from a flowJo workspace
getSamples-methods Get a list of samples from a flowJo workspace
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
getTotal-methods 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
getTransformations-methods Return a list of transformations or a transformation in a GatingHierarchy

-- I --

isNcdf determine the flow data associated with a Gating Hiearchy is based on 'ncdfFlowSet' or 'flowSet'

-- K --

keyword Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList'
keyword-method Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList'

-- L --

lapply apply 'FUN' to each sample (i.e. 'GatingHierarchy')
lapply-method apply 'FUN' to each sample (i.e. 'GatingHierarchy')
length Methods to get the length of a GatingSet
length-method Methods to get the length of a GatingSet
length-methods Methods to get the length of a GatingSet
load_gs save/load a GatingSet/GatingSetList to/from disk.
load_gslist save/load a GatingSet/GatingSetList to/from disk.

-- M --

mkformula make a formula from a character vector

-- N --

ncFlowSet Fetch the flowData object associated with a GatingSet .
ncFlowSet-method Fetch the flowData object associated with a GatingSet .
ncFlowSet<- Fetch the flowData object associated with a GatingSet .
ncFlowSet<--method Fetch the flowData object associated with a GatingSet .

-- O --

openWorkspace Open/Close a flowJo workspace
openWorkspace-method Open/Close a flowJo workspace
openWorkspace-methods Open/Close a flowJo workspace

-- P --

parseWorkspace Parse a flowJo Workspace
parseWorkspace-method Parse a flowJo Workspace
parseWorkspace-methods 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<--method read/set pData of flow data associated with 'GatingSet' or 'GatingSetList'
plot plot a GatingHierarchy
plot-method plot a GatingHierarchy
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.
plotPopCV-methods Plot the coefficient of variation between flowJo and flowCore population statistics for each population in a gating hierarchy.

-- R --

rbind2-method Class '"GatingSet"'
rbind2-method Class '"GatingSetList"'
recompute Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
recompute-method Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
Rm Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
Rm-method Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.

-- S --

sampleNames Get/update sample names in a GatingSet
sampleNames-method Class '"GatingSetList"'
sampleNames-method Get/update sample names in a GatingSet
sampleNames<--method Get/update sample names in a GatingSet
save_gs save/load a GatingSet/GatingSetList to/from disk.
save_gslist save/load a GatingSet/GatingSetList to/from disk.
setGate Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
setGate-method Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
setNode Update the name of one node in a gating hierarchy/GatingSet.
setNode-method Update the name of one node in a gating hierarchy/GatingSet.
show A class describing logical operation (& or |) of the reference populations
show-method Class GatingHierarchy
show-method Class '"GatingSet"'
show-method Class '"GatingSetList"'
show-method A class describing logical operation (& or |) of the reference populations
show-method An R representation of a flowJo workspace.
summary An R representation of a flowJo workspace.
summary-method An R representation of a flowJo workspace.

-- U --

unarchive archive/unarchive to/from a tar file

-- misc --

[ Class '"GatingSet"'
[-method Class '"GatingSet"'
[-method Class '"GatingSetList"'
[[ Class '"GatingSet"'
[[-method Class '"GatingSet"'
[[-method Class '"GatingSetList"'