Man pages for Bioconductor-mirror/flowWorkspace
Infrastructure for representing and interacting with the gated cytometry

addCreate a GatingSet and add/remove the flowCore gate(or...
asinh_Gml2inverse hyperbolic sine transform function generator...
asinhtGml2_transInverse hyperbolic sine transformation.
booleanFilter-classA class describing logical operation (& or |) of the...
checkRedundantNodestry to determine the redundant terminal(or leaf) nodes that...
cloneclone a GatingSet
compensatecompensate the flow data asssociated with the GatingSet
dropRedundantChannelsRemove the channels from flow data that are not used by gates
dropRedundantNodesRemove the terminal leaf nodes that make the gating trees to...
estimateLogicle.GatingHierarchyCompute logicle transformation from the flowData associated...
filterObjectconvert flowCore filter to a list It convert the flowCore...
flow_breaksGenerate the breaks that makes sense for flow data...
flowDataFetch or replace the flowData object associated with a...
flowJo_biexp_transflowJo biexponential transformation.
flowJo.fasinhinverse hyperbolic sine transform function
flowJo_fasinh_transflowJo inverse hyperbolic sine transformation.
flowJoTransconstruct the flowJo-type biexponentioal transformation...
flowJoWorkspace-classAn R representation of a flowJo workspace.
flow_transhelper function to generate a trans objects Used by other...
flowWorkspace-packageImport and replicate flowJo workspaces and gating schemes...
flowWorkspace.par.getflowWorkspace.par.set sets a set of parameters in the...
flowWorkspace.par.initworkspace version is parsed from xml node...
GatingHierarchy-classClass GatingHierarchy
GatingSet-classClass '"GatingSet"'
GatingSetList-classClass '"GatingSetList"'
GatingSet-methodsconstructors for GatingSet
getCompensationMatricesRetrieve the compensation matrices from a GatingHierarchy
getData-methodsget gated flow data from a...
getFJWSubsetIndicesFetch the indices for a subset of samples in a flowJo...
getGateReturn the flowCore gate definition associated with a node in...
getIndiceMatReturn the single-cell matrix of 1/0 dichotomized expression
getIndicesGet the membership indices for each event with respect to a...
getIndices-GatingSet-name-methodroutine to return the indices by specify boolean combination...
getKeywordsGet Keywords
getMergedStatsGet Cell Population Statistics and Sample Metadata
getNodesGet the names of all nodes from a gating hierarchy.
getParentReturn the name of the parent population or a list of child...
getPopStatsReturn a table of population statistics for all populations...
getSampleGroupsGet a table of sample groups from a flowJo workspace
getSamplesGet a list of samples from a flowJo workspace
getSingleCellExpressionReturn the cell events data that express in any of the single...
getTransformationsReturn a list of transformations or a transformation in a...
groupByChannelssplit GatingSets into groups based on their flow channels
groupByTreesplit GatingSets into groups based on their gating schemes Be...
insertGateinsert a dummy gate to the GatingSet
isNcdfdetermine the flow data associated with a Gating Hiearchy is...
keywordRetrieve a specific keyword for a specific sample in a...
lapply-methodsapply 'FUN' to each sample (i.e. 'GatingHierarchy')
lengthMethods to get the length of a GatingSet
logicleGml2_transGatingML2 version of logicle transformation.
logicle_translogicle transformation.
loglevelget/set the log level
markernamesGet/set the column(channel) or marker names
mkformulamake a formula from a character vector
moveNodemove a node along with all of its descendant nodes to the...
ncFlowSet-methodsFetch the flowData object associated with a GatingSet .
openWorkspaceOpen/Close a flowJo workspace
parseWorkspaceParse a flowJo Workspace
pData-methodsread/set pData of flow data associated with 'GatingSet' or...
plotGate-methodsPlot gates and associated cell population contained in a...
plot-methodsplot a gating tree
plotPopCVPlot the coefficient of variation between xml and openCyto...
prettyAxisDetermine tick mark locations and labels for a given channel...
recomputeCompute the cell events by the gates stored within the gating...
sampleNamesGet/update sample names in a GatingSet
save_gssave/load a GatingSet/GatingSetList to/from disk.
setGateupdate the gate
setNode-methodsUpdate the name of one node in a gating hierarchy/GatingSet.
standardize-GatingSetThe tools to standardize the tree structures and channel...
subsetsubset the GatingSet/GatingSetList based on 'pData'
transformtranform the flow data asssociated with the GatingSet
transformerListConstructor for transformerList object
updateChannelsUpdate the channel information of a GatingSet (c++ part)
Bioconductor-mirror/flowWorkspace documentation built on Aug. 2, 2017, 4:29 p.m.