Infrastructure for representing and interacting with the gated cytometry


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Documentation for package ‘flowWorkspace’ version 3.18.11

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A B C D F G I K L M N O P R S T 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.
asinhtGml2_trans Inverse hyperbolic sine transformation.
asinh_Gml2 inverse hyperbolic sine transform function generator (GatingML 2.0 version)

-- 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
checkRedundantNodes try to determine the redundant terminal(or leaf) nodes that can be removed
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
colnames-method Get/set the column(channel) or marker names
colnames<--method Get/set the column(channel) or marker names
compensate-method compensate the flow data asssociated with the GatingSet

-- D --

dropRedundantChannels Remove the channels from flow data that are not used by gates
dropRedundantNodes Remove the terminal leaf nodes that make the gating trees to be different from one another.

-- F --

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

-- G --

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!!

-- I --

insertGate insert a dummy gate to the GatingSet
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-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
load_gs save/load a GatingSet/GatingSetList to/from disk.
load_gslist save/load a GatingSet/GatingSetList to/from disk.
logicleGml2_trans GatingML2 version of logicle transformation.
logicle_trans logicle transformation.

-- M --

markernames-method Get/set the column(channel) or marker names
markernames<--method Get/set the column(channel) or marker names
merge-GatingSet The tools to standardize the tree structures and channel names.
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

-- P --

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

-- R --

rbind2-method Class '"GatingSetList"'
recompute Compute the cell events by the gates stored within the gating tree
recompute-method Compute the cell events by the gates stored within the gating tree
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 Get/update sample names in a GatingSet
sampleNames<- 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 update the gate
setGate-method update the gate
setLoglevel get/set the log level
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-method Class GatingHierarchy
show-method A class describing logical operation (& or |) of the reference populations
show-method An R representation of a flowJo workspace.
show-method Methods to get the length of a GatingSet
standardize-GatingSet The tools to standardize the tree structures and channel names.
subset.GatingSet subset the GatingSet/GatingSetList based on 'pData'

-- T --

transform-method tranform the flow data asssociated with the GatingSet
transformerList Constructor for transformerList object

-- U --

updateChannels Update the channel information of a GatingSet (c++ part)

-- misc --

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