Infrastructure for representing and interacting with the gated cytometry

Documentation for package ‘flowWorkspace’ version 3.26.2

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

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.

-- E --

estimateLogicle.GatingHierarchy

Compute logicle transformation from the flowData associated with a GatingHierarchy

-- F --

filterObject	convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure.
filterObject-method	convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure.
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
getMergedStats	Get Cell Population Statistics and Sample Metadata
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'
getSingleCellExpressionByGate	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
moveNode	move a node along with all of its descendant nodes to the given ancester

-- 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 xml and openCyto population statistics for each population in a gating hierarchy.
plotPopCV-method	Plot the coefficient of variation between xml and openCyto 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.
set.count.xml	save the event counts parsed from xml into c++ tree structure
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"'