Man pages for RGLab/flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.

asinh_Gml2inverse hyperbolic sine transform function generator...
asinhtGml2_transInverse hyperbolic sine transformation.
booleanFilter-classA class describing logical operation (& or |) of the...
bracketsBracket operators on 'GatingSet' and 'GatingSetList' objects
cf_append_colsAppend data columns to a flowFrame
cf_backend_typereturn the cytoframe backend storage format
cf_get_uriReturn the file path of the underlying h5 file
cf_write_diskSave the cytoframe to disk
cf_write_h5Save the cytoframe as h5 format
cf_write_tileSave the cytoframe as h5 format
cleanupRemove on-disk files associatated with flowWorkspace data...
cleanup_tempRemove temporary files associatated with flowWorkspace data...
compensatecompensate the flow data asssociated with the GatingSet
convertMethods for conversion between flowCore and flowWorkspace...
convert_backendconvert h5 based gs archive to tiledb
convert_legacyconvert the legacy GatingSet archive (mixed with R and C++...
cs_add_cytoframeAdd a cytoframe to a cytoset
cs_get_uriReturn the path of the underlying data files
cs_set_cytoframeupdate a cytoframe in a cytoset
cytoframe'cytoframe': A reference class for efficiently managing the...
cytoframe-keywords'cytoframe' keyword access methods
cytoframe-labelsMethods to change channel and marker names for 'cytoframe'...
cytoset'cytoset': a reference class for efficiently managing the...
default_backendget/set the default backend format of cytoframe
delete_gsdelete the archive of GatingSet
estimateLogicleCompute logicle transformation from the flowData associated...
extract_cluster_pop_name_from_nodeExtract the population name from the node path It strips the...
filter_to_listconvert flowCore filter to a list It convert the flowCore...
flow_breaksGenerate the breaks that makes sense for flow data...
flowjo_biexpconstruct the flowJo-type biexponentioal transformation...
flowjo_biexp_transflowJo biexponential transformation.
flowjo_fasinhinverse hyperbolic sine transform function
flowjo_fasinh_transflowJo inverse hyperbolic sine transformation.
flowjo_log_transflog transform function
flow_transhelper function to generate a trans objects Used by other...
flowWorkspace-deprecatedDeprecated functions in package 'flowWorkspace'.
flowWorkspace-packageImport and replicate flowJo workspaces and gating schemes...
GatingHierarchy-classClass GatingHierarchy
GatingSet-classClass '"GatingSet"'
GatingSetList-classClass '"GatingSetList"'
GatingSet-methodsconstructors for GatingSet
gh_apply_to_new_fcsconstructors for GatingSet
gh_copy_gateCopy a node along with all of its descendant nodes to the...
gh_get_cluster_labelsRetrieve the cluster labels from the cluster nodes
gh_get_compensationsRetrieve the compensation matrices from a 'GatingHierarchy'...
gh_get_transformationsReturn a list of transformations or a transformation in a...
gh_pop_compare_statsCompare the stats(count/freq) between the version parsed from...
gh_pop_get_cluster_namecheck if a node is clustering node
gh_pop_get_dataget gated flow data from a...
gh_pop_get_descendantsget all the descendant nodes for the given ancester
gh_pop_get_full_pathconvert the partial gating path to the full path
gh_pop_get_indicesGet the membership indices for each event with respect to a...
gh_pop_get_indices_matReturn the single-cell matrix of 1/0 dichotomized expression
gh_pop_get_proportionGet count or proportion from populations
gh_pop_movemove a node along with all of its descendant nodes to the...
gh_pop_set_indicesdirectly update event indices without changing gates
gh_pop_set_xml_countsave the event counts parsed from xml into c++ tree structure
gs_check_redundant_nodestry to determine the redundant terminal(or leaf) nodes that...
gs_cyto_dataFetch or replace the flowData object associated with a...
gs_get_compensation_internalextract compensation object from GatingSet
gs_get_leaf_nodesget all the leaf nodes
gs_get_pop_pathsGet the names of all nodes from a gating hierarchy.
gs_get_singlecell_expressionReturn the cell events data that express in any of the single...
gs_is_persistentdetermine whether the flow data associated with a GatingSet...
gslist_to_gsMerge a GatingSetList into a single GatingSet
gs_plot_diff_treevisualize the tree structure differnece among the GatingSets
gs_plot_pop_count_cvPlot the coefficient of variation between xml and openCyto...
gs_pop_addCreate a GatingSet and add/remove the flowCore gate(or...
gs_pop_get_childrenReturn the name of the parent population or a list of child...
gs_pop_get_count_fastReturn a table of population statistics for all populations...
gs_pop_get_gateReturn the flowCore gate definition associated with a node in...
gs_pop_get_statsExtract stats from populations(or nodes)
gs_pop_get_stats_tfilterExtract stats from populations(or nodes) within a restricted...
gs_pop_set_gateupdate the gate
gs_pop_set_nameUpdate the name of one node in a gating hierarchy/GatingSet.
gs_pop_set_visibilityhide/unhide a node
gs_remove_redundant_channelsRemove the channels from flow data that are not used by gates
gs_remove_redundant_nodesRemove the terminal leaf nodes that make the gating trees to...
gs_split_by_channelssplit GatingSets into groups based on their flow channels
gs_split_by_treesplit GatingSets into groups based on their gating schemes Be...
gs_update_channelsUpdate the channel information of a GatingSet (c++ part)
identifier-methodsRetrieve/replace the GUID of a GatingSet or GatingSetList
is_tiledb_supportcheck whether cytolib is build with tiledb support
keywordRetrieve a specific keyword for a specific sample in a...
lapply-methodsapply 'FUN' to each sample (i.e. 'GatingHierarchy' or...
lengthMethods to get the length of a GatingSet
load_cytoframeLoad the cytoframe from disk
load_cytoframe_from_fcsRead a single FCS file in to a cytoframe
load_cytoset_from_fcsRead one or several FCS files in to a cytoset
load_metaFlush/load meta data (keywords, pData, channels/markers)...
lockLock/Unlock the cytoset/cytoframe by turning on/off its...
logicleGml2_transGatingML2 version of logicle transformation.
logicle_translogicle transformation.
loglevelget/set the log level
logtGml2_transGating-ML 2.0 Log transformation.
markernamesGet/set the column(channel) or marker names
merge_list_to_gsMerge a list of GatingSets into a single GatingSet
ncFlowSet-methodsFetch the flowData object associated with a GatingSet .
nodeflagsThe flags of gate nodes
openWorkspaceIt is now moved along with entire flowJo parser to CytoML...
pData-methodsread/set pData of flow data associated with...
plotGate-methods-defunctPlot gates and associated cell population contained in a...
plot-methodsplot a gating tree
pop_addAdd populations to a GatingHierarchy
prettyAxisDetermine tick mark locations and labels for a given channel...
recomputeCompute the cell events by the gates stored within the gating...
rotate_gateSimplified geometric rotation of gates associated with nodes
sampleNamesGet/update sample names in a GatingSet
save_cytosetsave/load a cytoset to/from disk.
save_gssave/load a GatingSet/GatingSetList to/from disk.
scale_gateSimplified geometric scaling of gates associated with nodes
shift_gateSimplified geometric translation of gates associated with...
standardize-GatingSetThe tools to standardize the tree structures and channel...
stats.funbuilt-in stats functions.
subsetsubset the GatingSet/GatingSetList based on 'pData'
swap_data_colsSwap the colnames Perform some validity checks before...
transformtranform the flow data asssociated with the GatingSet
transformerListConstructor for transformerList object
transform_gateSimplified geometric transformations of gates associated with...
RGLab/flowWorkspace documentation built on July 9, 2020, 1:55 a.m.