getData,GatingHierarchy,missing-method {flowWorkspace}R Documentation

get gated flow data from a GatingHierarchy/GatingSet/GatingSetList

Description

get gated flow data from a GatingHierarchy/GatingSet/GatingSetList

Usage

## S4 method for signature 'GatingHierarchy,missing'
getData(obj, y, ...)

## S4 method for signature 'GatingHierarchy,character'
getData(obj, y, ...)

## S4 method for signature 'GatingSet,missing'
getData(obj, y, ...)

## S4 method for signature 'GatingSet,character'
getData(obj, y, ...)

## S4 method for signature 'GatingSetList,ANY'
getData(obj, y, ...)

Arguments

obj

A GatingHierarchy, GatingSet or GatingSetList object.

y

character the node name or full(/partial) gating path. If not specified, will return the complete flowFrame/flowSet at the root node.

...

arguments passed to ncdfFlow::[[

Details

Returns a flowFrame/flowSet containing the events in the gate defined at node y. Subset membership can be obtained using getIndices. Population statistics can be obtained using getPop and getPopStats. When calling getData on a GatingSet,the trees representing the GatingHierarchy for each sample in the GaingSet are presumed to have the same structure. To update the data, use flowData method.

Value

A flowFrame object if obj is a GatingHierarchy. A flowSet or ncdfFlowSet if a GatingSet. A ncdfFlowList if a GatingSetList.

See Also

flowData getIndices getPopStats

Examples

  ## Not run: 
    #G is a GatingSet
    geData(G,3) #get a flowSet constructed from the third node / population in the tree.
    geData(G,"cd4")

    #gh is a GatingHierarchy
    getData(gh)

## End(Not run)
[Package flowWorkspace version 3.26.9 Index]