get gated flow data from a GatingHierarchy/GatingSet/GatingSetList

get gated flow data from a GatingHierarchy/GatingSet/GatingSetList

gh_pop_get_data(obj, y = "root", inverse.transform = FALSE, ...)

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.
inverse.transform	logical flag indicating whether to inverse transform the data
...	arguments passed to ncdfFlow::[[

Value

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

Details

Returns a flowFrame/flowSet containing the events in the gate defined at node y. Subset membership can be obtained using gh_pop_get_indices. Population statistics can be obtained using getPop and gh_pop_compare_stats. When calling gh_pop_get_data 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 gs_cyto_data method.

See also

gs_cyto_data gh_pop_get_indices gh_pop_compare_stats

Examples

  if (FALSE) {
    #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
    gh_pop_get_data(gh)
}