Infrastructure for representing and interacting with gated and ungated cytometry data sets.

---

Documentation for package ‘flowWorkspace’ version 4.19.1

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

Help Pages

A B C D E 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
brackets	Bracket operators on 'GatingSet' and 'GatingSetList' objects

-- C --

cf_append_cols	Append data columns to a flowFrame
cf_backend_type	return the cytoframe backend storage format
cf_cleanup	Remove on-disk files associatated with flowWorkspace data classes
cf_cleanup_temp	Remove temporary files associatated with flowWorkspace data classes
cf_flush_meta	Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
cf_get_h5_file_path	Return the file path of the underlying h5 file
cf_get_uri	Return the file path of the underlying h5 file
cf_is_subsetted	check whether a cytoframe/cytoset is a subsetted(by column or by row) view
cf_keyword_delete	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cf_keyword_insert	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cf_keyword_rename	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cf_keyword_set	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cf_load_meta	Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
cf_lock	Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
cf_rename_channel	Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cf_rename_marker	Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cf_swap_colnames	Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cf_unlock	Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
cf_write_disk	Save the cytoframe to disk
cf_write_h5	Save the cytoframe as h5 format
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
cleanup	Remove on-disk files associatated with flowWorkspace data classes
cleanup_temp	Remove temporary files associatated with flowWorkspace data classes
colnames-method	Get/set the column(channel) or marker names
colnames<--method	Get/set the column(channel) or marker names
compensate	compensate the flow data asssociated with the GatingSet
compensate-method	compensate the flow data asssociated with the GatingSet
convert	Methods for conversion between flowCore and flowWorkspace data classes
convert_backend	convert h5 based gs archive to tiledb
convert_legacy_gs	convert the legacy GatingSet archive (mixed with R and C++ files) to the new format (C++ only)
convert_legacy_gslist	convert the legacy GatingSet archive (mixed with R and C++ files) to the new format (C++ only)
copyNode	Copy a node along with all of its descendant nodes to the given ancestor
cs_add_cytoframe	Add a cytoframe to a cytoset
cs_cleanup	Remove on-disk files associatated with flowWorkspace data classes
cs_cleanup_temp	Remove temporary files associatated with flowWorkspace data classes
cs_flush_meta	Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
cs_get_cytoframe	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
cs_get_h5_file_path	Return the path of the underlying data files
cs_get_uri	Return the path of the underlying data files
cs_is_subsetted	check whether a cytoframe/cytoset is a subsetted(by column or by row) view
cs_keyword_delete	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cs_keyword_insert	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cs_keyword_rename	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cs_keyword_set	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cs_load_meta	Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
cs_lock	Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
cs_set_cytoframe	update a cytoframe in a cytoset
cs_swap_colnames	Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cs_unlock	Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
cytoframe	'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
cytoframe-class	'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
cytoframe-labels	Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cytoframe_to_flowFrame	Methods for conversion between flowCore and flowWorkspace data classes
cytoset	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
cytoset-class	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
cytoset_to_flowSet	Methods for conversion between flowCore and flowWorkspace data classes
cytoset_to_list	Methods for conversion between flowCore and flowWorkspace data classes

-- D --

delete_gs	delete the archive of GatingSet
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	Compute logicle transformation from the flowData associated with a GatingHierarchy
estimateLogicle-method	Compute logicle transformation from the flowData associated with a GatingHierarchy
estimateLogicle.GatingHierarchy	Compute logicle transformation from the flowData associated with a GatingHierarchy
extract_cluster_pop_name_from_node	Extract the population name from the node path It strips the parent path and cluster method name.

-- 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.
filter_to_list	convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure.
filter_to_list-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 .
flowFrame_to_cytoframe	Methods for conversion between flowCore and flowWorkspace data classes
flowJo.fasinh	inverse hyperbolic sine transform function
flowJo.flog	flog transform function
flowJo.fsinh	inverse hyperbolic sine transform function
flowJoTrans	construct the flowJo-type biexponentioal transformation function
flowjo_biexp	construct the flowJo-type biexponentioal transformation function
flowJo_biexp_trans	flowJo biexponential transformation.
flowjo_biexp_trans	flowJo biexponential transformation.
flowjo_fasinh	inverse hyperbolic sine transform function
flowJo_fasinh_trans	flowJo inverse hyperbolic sine transformation.
flowjo_fasinh_trans	flowJo inverse hyperbolic sine transformation.
flowjo_flog	flog transform function
flowjo_fsinh	inverse hyperbolic sine transform function
flowjo_log_trans	flog transform function
flowSet_to_cytoset	Methods for conversion between flowCore and flowWorkspace data classes
flowSet_to_list	Methods for conversion between flowCore and flowWorkspace data classes
flowWorkspace	Import and replicate flowJo workspaces and gating schemes using flowCore.
flowWorkspace-deprecated	Deprecated functions in package 'flowWorkspace'.
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
flush_meta	Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)

-- G --

GatingHierarchy	Class GatingHierarchy
GatingHierarchy-class	Class GatingHierarchy
GatingSet	Class '"GatingSet"'
GatingSet-class	Class '"GatingSet"'
GatingSet-method	constructors for GatingSet
GatingSet-method	Construct a 'GatingSet' using a template
GatingSet-methods	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' or 'GatingSet'
getCompensationMatrices-method	Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet'
getData	get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
getData-method	get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
getDescendants	get all the descendant nodes for the given ancester
getDescendants-method	get all the descendant nodes for the given ancester
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.
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
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	Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R
getPopStats-method	Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R
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	Get count or proportion from populations
getSingleCellExpression	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'
getStats	Extract stats from populations(or nodes)
getStats-method	Extract stats from populations(or nodes)
getTotal	Get count or proportion from populations
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
get_cytoframe_from_cs	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
get_default_backend	get/set the default backend format of cytoframe
get_leaf_nodes	get all the leaf nodes
get_log_level	get/set the log level
gh_apply_to_cs	Construct a 'GatingSet' using a template
gh_apply_to_new_fcs	Construct a 'GatingSet' using a template and FCS files
gh_cleanup	Remove on-disk files associatated with flowWorkspace data classes
gh_cleanup_temp	Remove temporary files associatated with flowWorkspace data classes
gh_copy_gate	Copy a node along with all of its descendant nodes to the given ancestor
gh_get_cluster_labels	Retrieve the cluster labels from the cluster nodes
gh_get_compensations	Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet'
gh_get_leaf_nodes	get all the leaf nodes
gh_get_pop_paths	Get the names of all nodes from a gating hierarchy.
gh_get_transformations	Return a list of transformations or a transformation in a GatingHierarchy
gh_keyword_delete	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gh_keyword_insert	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gh_keyword_rename	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gh_keyword_set	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gh_plot_pop_count_cv	Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy.
gh_pop_compare_stats	Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R
gh_pop_get_children	Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
gh_pop_get_cluster_name	check if a node is clustering node
gh_pop_get_count	Get count or proportion from populations
gh_pop_get_data	get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
gh_pop_get_descendants	get all the descendant nodes for the given ancester
gh_pop_get_full_path	convert the partial gating path to the full path
gh_pop_get_gate	Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.
gh_pop_get_indices	Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
gh_pop_get_indices_mat	Return the single-cell matrix of 1/0 dichotomized expression
gh_pop_get_parent	Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
gh_pop_get_proportion	Get count or proportion from populations
gh_pop_get_stats	Extract stats from populations(or nodes)
gh_pop_get_stats_tfilter	Extract stats from populations(or nodes) within a restricted time window
gh_pop_is_bool_gate	The flags of gate nodes
gh_pop_is_gated	The flags of gate nodes
gh_pop_is_hidden	The flags of gate nodes
gh_pop_is_negated	The flags of gate nodes
gh_pop_move	move a node along with all of its descendant nodes to the given ancester
gh_pop_remove	Add populations to a GatingHierarchy
gh_pop_set_gate	update the gate
gh_pop_set_indices	directly update event indices without changing gates
gh_pop_set_name	Update the name of one node in a gating hierarchy/GatingSet.
gh_pop_set_visibility	hide/unhide a node
gh_pop_set_xml_count	save the event counts parsed from xml into c++ tree structure
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!!
gslist_to_gs	Merge a GatingSetList into a single GatingSet
gs_check_redundant_nodes	try to determine the redundant terminal(or leaf) nodes that can be removed
gs_cleanup	Remove on-disk files associatated with flowWorkspace data classes
gs_cleanup_temp	Remove temporary files associatated with flowWorkspace data classes
gs_cyto_data	Fetch or replace the flowData object associated with a GatingSet .
gs_cyto_data-method	Fetch or replace the flowData object associated with a GatingSet .
gs_cyto_data<-	Fetch or replace the flowData object associated with a GatingSet .
gs_cyto_data<--method	Fetch or replace the flowData object associated with a GatingSet .
gs_get_compensations	Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet'
gs_get_compensation_internal	extract compensation object from GatingSet
gs_get_cytoframe	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
gs_get_leaf_nodes	get all the leaf nodes
gs_get_pop_paths	Get the names of all nodes from a gating hierarchy.
gs_get_singlecell_expression	Return the cell events data that express in any of the single populations defined in 'y'
gs_get_singlecell_expression_by_gate	Return the cell events data that express in any of the single populations defined in 'y'
gs_get_uri	Return the path of the underlying data files
gs_is_h5	determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory
gs_is_persistent	determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory
gs_keyword_delete	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gs_keyword_insert	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gs_keyword_rename	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gs_keyword_set	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gs_plot_diff_tree	visualize the tree structure differnece among the GatingSets
gs_plot_pop_count_cv	Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy.
gs_pop_add	Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
gs_pop_get_children	Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
gs_pop_get_count_fast	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
gs_pop_get_count_with_meta	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
gs_pop_get_data	get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
gs_pop_get_gate	Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.
gs_pop_get_gs	subset gs by population node
gs_pop_get_parent	Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
gs_pop_get_stats	Extract stats from populations(or nodes)
gs_pop_get_stats_tfilter	Extract stats from populations(or nodes) within a restricted time window
gs_pop_remove	Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
gs_pop_set_gate	update the gate
gs_pop_set_name	Update the name of one node in a gating hierarchy/GatingSet.
gs_pop_set_visibility	hide/unhide a node
gs_remove_redundant_channels	Remove the channels from flow data that are not used by gates
gs_remove_redundant_nodes	Remove the terminal leaf nodes that make the gating trees to be different from one another.
gs_split_by_channels	split GatingSets into groups based on their flow channels
gs_split_by_tree	split GatingSets into groups based on their gating schemes Be careful that the splitted resluts still points to the original data set!!
gs_update_channels	Update the channel information of a GatingSet (c++ part)

-- I --

identifier	Retrieve/replace the GUID of a GatingSet or GatingSetList
identifier-method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
identifier-method	Retrieve/replace the GUID of a GatingSet or GatingSetList
identifier-methods	Retrieve/replace the GUID of a GatingSet or GatingSetList
identifier<--method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
identifier<--method	Retrieve/replace the GUID of a GatingSet or GatingSetList
isGated	The flags of gate nodes
isHidden	The flags of gate nodes
isNcdf	determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory
isNegated	The flags of gate nodes

-- 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	'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
keyword-method	Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList'
keyword-mutators	Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects

-- L --

lapply	apply 'FUN' to each sample (i.e. 'GatingHierarchy' or 'cytoframe') in a 'GatingSet' or 'cytoset'
lapply-method	apply 'FUN' to each sample (i.e. 'GatingHierarchy' or 'cytoframe') in a 'GatingSet' or 'cytoset'
lapply-methods	apply 'FUN' to each sample (i.e. 'GatingHierarchy' or 'cytoframe') in a 'GatingSet' or 'cytoset'
length	Methods to get the length of a GatingSet
length-method	Methods to get the length of a GatingSet
load_cytoframe	Load the cytoframe from disk
load_cytoframe_from_fcs	Read a single FCS file in to a cytoframe
load_cytoset	save/load a cytoset to/from disk.
load_cytoset_from_fcs	Read one or several FCS files in to a cytoset
load_gs	save/load a GatingSet/GatingSetList to/from disk.
load_gslist	save/load a GatingSet/GatingSetList to/from disk.
load_meta	Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
lock	Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
logicleGml2_trans	GatingML2 version of logicle transformation.
logicle_trans	logicle transformation.
logtGml2_trans	Gating-ML 2.0 Log transformation.

-- M --

markernames	Get/set the column(channel) or marker names
markernames-method	'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
markernames-method	Get/set the column(channel) or marker names
markernames<--method	'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
markernames<--method	Get/set the column(channel) or marker names
markernmaes<--method	Get/set the column(channel) or marker names
merge-GatingSet	The tools to standardize the tree structures and channel names.
merge_list_to_gs	Merge a list of GatingSets into a single GatingSet
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 .
nodeflags	The flags of gate nodes

-- O --

openWorkspace

It is now moved along with entire flowJo parser to CytoML package

-- P --

pData	read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
pData-method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
pData-method	read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
pData-methods	read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
pData<-	read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
pData<--method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
pData<--method	read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
phenoData-method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
phenoData<--method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
plot	plot a gating tree
plot-method	plot a gating tree
plot-methods	plot a gating tree
pop.MFI	built-in stats functions.
pop_add	Add populations to a GatingHierarchy
pop_add.factor	Add populations to a GatingHierarchy
pop_add.filter	Add populations to a GatingHierarchy
pop_add.filters	Add populations to a GatingHierarchy
pop_add.logical	Add populations to a GatingHierarchy
pop_add.logicalFilterResult	Add populations to a GatingHierarchy
pop_add.multipleFilterResult	Add populations to a GatingHierarchy
pop_add.quadGate	Add populations to a GatingHierarchy
prettyAxis	Determine tick mark locations and labels for a given channel axis

-- R --

rbind2-method	Merge a GatingSetList into a single GatingSet
realize_view	'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
realize_view-method	'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
realize_view-method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
recompute	Compute the cell events by the gates stored within the gating tree.
recompute.GatingSet	Compute the cell events by the gates stored within the gating tree.
recompute.GatingSetList	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.
rotate_gate	Simplified geometric rotation of gates associated with nodes
rotate_gate-method	Simplified geometric rotation of gates associated with nodes
rotate_gate.GatingHierarchy	Simplified geometric rotation of gates associated with nodes

-- S --

sampleNames	Get/update sample names in a GatingSet
sampleNames,cytoset,	Get/update sample names in a GatingSet
sampleNames-method	Get/update sample names in a GatingSet
sampleNames-method	save/load a GatingSet/GatingSetList to/from disk.
sampleNames<-	Get/update sample names in a GatingSet
sampleNames<--method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
sampleNames<--method	Get/update sample names in a GatingSet
save_cytoset	save/load a cytoset to/from disk.
save_gs	save/load a GatingSet/GatingSetList to/from disk.
save_gslist	save/load a GatingSet/GatingSetList to/from disk.
scale_gate	Simplified geometric scaling of gates associated with nodes
scale_gate-method	Simplified geometric scaling of gates associated with nodes
scale_gate.GatingHierarchy	Simplified geometric scaling of gates associated with nodes
setGate	update the gate
setGate-method	update the gate
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.
setNode-method	hide/unhide a node
set_default_backend	get/set the default backend format of cytoframe
set_log_level	get/set the log level
shift_gate	Simplified geometric translation of gates associated with nodes
shift_gate-method	Simplified geometric translation of gates associated with nodes
shift_gate.GatingHierarchy	Simplified geometric translation of gates associated with nodes
show-method	Class GatingHierarchy
show-method	A class describing logical operation (& or |) of the reference populations
show-method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
show-method	Methods to get the length of a GatingSet
standardize-GatingSet	The tools to standardize the tree structures and channel names.
stats.fun	built-in stats functions.
subset	subset the GatingSet/GatingSetList based on 'pData'
subset.GatingSet	subset the GatingSet/GatingSetList based on 'pData'
swap_data_cols	Swap the colnames Perform some validity checks before returning the updated colnames

-- T --

transform	tranform the flow data asssociated with the GatingSet
transform-method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
transform-method	tranform the flow data asssociated with the GatingSet
transformerList	Constructor for transformerList object
transform_gate	Simplified geometric transformations of gates associated with nodes
transform_gate-method	Simplified geometric transformations of gates associated with nodes
transform_gate.GatingHierarchy	Simplified geometric transformations of gates associated with nodes

-- U --

updateChannels	Update the channel information of a GatingSet (c++ part)
updateIndices	directly update event indices without changing gates
updateIndices-method	directly update event indices without changing gates

-- misc --

[	Bracket operators on 'GatingSet' and 'GatingSetList' objects
[-method	Bracket operators on 'GatingSet' and 'GatingSetList' objects
[-method	'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
[-method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
[[	Bracket operators on 'GatingSet' and 'GatingSetList' objects
[[-method	Bracket operators on 'GatingSet' and 'GatingSetList' objects
[[-method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
[[<--method	Bracket operators on 'GatingSet' and 'GatingSetList' objects
[[<--method	'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'