Infrastructure for representing and interacting with the gated cytometry

add | Create a GatingSet and add/remove the flowCore gate(or... |

asinh_Gml2 | inverse hyperbolic sine transform function generator... |

asinhtGml2_trans | Inverse hyperbolic sine transformation. |

booleanFilter-class | A class describing logical operation (& or |) of the... |

checkRedundantNodes | try to determine the redundant terminal(or leaf) nodes that... |

clone | clone a GatingSet |

compensate | compensate the flow data asssociated with the 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... |

estimateLogicle.GatingHierarchy | Compute logicle transformation from the flowData associated... |

filterObject | convert flowCore filter to a list It convert the flowCore... |

flow_breaks | Generate the breaks that makes sense for flow data... |

flowData | Fetch or replace the flowData object associated with a... |

flowJo_biexp_trans | flowJo biexponential transformation. |

flowJo.fasinh | inverse hyperbolic sine transform function |

flowJo_fasinh_trans | flowJo inverse hyperbolic sine transformation. |

flowJoTrans | construct the flowJo-type biexponentioal transformation... |

flowJoWorkspace-class | An R representation of a flowJo workspace. |

flow_trans | helper function to generate a trans objects Used by other... |

flowWorkspace-package | Import and replicate flowJo workspaces and gating schemes... |

flowWorkspace.par.get | flowWorkspace.par.set sets a set of parameters in the... |

flowWorkspace.par.init | workspace version is parsed from xml node... |

GatingHierarchy-class | Class GatingHierarchy |

GatingSet-class | Class '"GatingSet"' |

GatingSetList-class | Class '"GatingSetList"' |

GatingSet-methods | constructors for GatingSet |

getCompensationMatrices | Retrieve the compensation matrices from a GatingHierarchy |

getData-methods | get gated flow data from a... |

getFJWSubsetIndices | Fetch the indices for a subset of samples in a flowJo... |

getGate | Return the flowCore gate definition associated with a node in... |

getIndiceMat | Return the single-cell matrix of 1/0 dichotomized expression |

getIndices | Get the membership indices for each event with respect to a... |

getIndices-GatingSet-name-method | routine to return the indices by specify boolean combination... |

getKeywords | Get Keywords |

getMergedStats | Get Cell Population Statistics and Sample Metadata |

getNodes | Get the names of all nodes from a gating hierarchy. |

getParent | Return the name of the parent population or a list of child... |

getPopStats | Return a table of population statistics for all populations... |

getSampleGroups | Get a table of sample groups from a flowJo workspace |

getSamples | Get a list of samples from a flowJo workspace |

getSingleCellExpression | Return the cell events data that express in any of the single... |

getTransformations | Return a list of transformations or a transformation in a... |

groupByChannels | split GatingSets into groups based on their flow channels |

groupByTree | split GatingSets into groups based on their gating schemes Be... |

insertGate | insert a dummy gate to the GatingSet |

isNcdf | determine the flow data associated with a Gating Hiearchy is... |

keyword | Retrieve a specific keyword for a specific sample in a... |

lapply-methods | apply 'FUN' to each sample (i.e. 'GatingHierarchy') |

length | Methods to get the length of a GatingSet |

logicleGml2_trans | GatingML2 version of logicle transformation. |

logicle_trans | logicle transformation. |

loglevel | get/set the log level |

markernames | Get/set the column(channel) or marker names |

mkformula | make a formula from a character vector |

moveNode | move a node along with all of its descendant nodes to the... |

ncFlowSet-methods | Fetch the flowData object associated with a GatingSet . |

openWorkspace | Open/Close a flowJo workspace |

parseWorkspace | Parse a flowJo Workspace |

pData-methods | read/set pData of flow data associated with 'GatingSet' or... |

plotGate-methods | Plot gates and associated cell population contained in a... |

plot-methods | plot a gating tree |

plotPopCV | Plot the coefficient of variation between xml and openCyto... |

prettyAxis | Determine tick mark locations and labels for a given channel... |

recompute | Compute the cell events by the gates stored within the gating... |

sampleNames | Get/update sample names in a GatingSet |

save_gs | save/load a GatingSet/GatingSetList to/from disk. |

setGate | update the gate |

setNode-methods | Update the name of one node in a gating hierarchy/GatingSet. |

standardize-GatingSet | The tools to standardize the tree structures and channel... |

subset | subset the GatingSet/GatingSetList based on 'pData' |

transform | tranform the flow data asssociated with the GatingSet |

transformerList | Constructor for transformerList object |

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

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