flowWorkspace (version 3.16.0)

GatingSet-class: Class "GatingSet"

Description

GatingSet holds a set of GatingHierarchy objects, representing a set of samples and the gating scheme associated with each.

[ subsets a GatingSet or GatingSetList using the familiar bracket notation

[[ extract a GatingHierarchy object from a GatingSet or GatingSetList

Usage

"["(x, i, j, ..., drop = TRUE)
"[["(x, i, j, ...)
"["(x, i, j, ..., drop = TRUE)

Arguments

x

GatingSet or GatingSetList

i

numeric or logical or character used as sample index

j

not used

...

not used

drop

not used

Slots

FCSPath:

deprecated

data:

Object of class "flowSet". flow data associated with this GatingSet

flag:

Object of class "logical". A flag indicating whether the gates, transformations, and compensation matrices have been applied to data, or simply imported.

axis:

Object of class "list". stores the axis information used for plotGate.

pointer:

Object of class "externalptr". points to the gating hierarchy stored in C data structure.

guid:

Object of class "character". the unique identifier for GatingSet object.

Details

Objects stores a collection of GatingHierarchies and represent a group in a flowJo workspace. A GatingSet can have two ``states''. After a call to parseWorkspace(...,execute=FALSE) , the workspace is imported but the data is not. Setting execute to TRUE is needed in order to load, transform, compensate, and gate the associated data. Whether or not a GatingHierarchy has been applied to data is encoded in the flag slot. Some methods will warn the user, or may not function correctly if the GatingHierarchy has not been executed. This mechanism is in place, largely for the purpose of speed when working with larger workspaces. It allows the use to load a workspace and subset desired samples before proceeding to load the data.

See Also

GatingHierarchy flowJoWorkspace parseWorkspace

Examples

require(flowWorkspaceData)
  d<-system.file("extdata",package="flowWorkspaceData")
  wsfile<-list.files(d,pattern="A2004Analysis.xml",full=TRUE)
  ws <- openWorkspace(wsfile);
  G<-try(parseWorkspace(ws,execute=TRUE,path=d,name=1));
  plotPopCV(G);