gateSet-class {prada} | R Documentation

## 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data

### Description

In flow-cytometry analysis, regions in two-dimensional projections of the data space often have to be selected. Objects of this class can store the properties for several of these selections

### Creating Objects

Objects can be created using methods of the generic function `drawGate` or via
`new("gateSet",`
`glist = ...., # object of class list`
`)`

### Slots

`name`:
  Object of class `character` giving the name of the object. You can reference the object by its name for subsequent operations (e.g. plotting).
`glist`:
  Object of class `"list"` with items of class `gate`. The individual `gate` objects will be combined according to the value of their slot `logic`.

### Methods

applyGate:
  `applyGate(x, data)`
  applies the gating of object `x` on data objects of class `cytoFrame` or `matrix`.
length
  length of slot `glist`.
show
  `display summary`
names, names<-
  extract or replace the names of the individual `gate` objects.
[
  subset to `gateSet` objects.
[[
  subset to individual `gate` objects.

appendGates
  append a `gate` or `gateSet` to a `cytoFrame`

### Author(s)

Florian Hahne

### See Also

`cytoFrame`, `gateMatrix`, `gate`

### Examples

    sampdat <- readFCS(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                                   package="prada"))
    g1 <- new("gate", name="G1", gateFun=function(x)x[,"FSC-H"]<500, logic="&",
              colnames="FSC-H")
    g2 <- new("gate", name="G2", gateFun=function(x)x[,"SSC-H"]>800, logic="&",
              colnames="SSC-H")
    g3 <- new("gate", name="G3", gateFun=function(x)x[,"FL1-H"]>800, logic="&",
              colnames="FL1-H")
    gs <- new("gateSet", name="Set1", glist=list(G1=g1, G2=g2))
    length(gs)
    gs[[1]]
    gs[1]
    gsnames <- names(gs)
    names(gs) <- gsnames
    applyGate(sampdat, gs)
    applyGate(exprs(sampdat), gs)
    gate(sampdat) <- gs
    applyGate(sampdat, 1)
    applyGate(sampdat, "G1")
    applyGate(sampdat, TRUE)
    appendGates(sampdat, g3)

[Package prada version 1.10.1 Index]