# Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore

## Documentation for package ‘flowWorkspace’ version 3.8.61

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"'