gate-class {prada} | R Documentation

## 'gate': a class for subsetting flow-cytometry data by defining 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 of these selections.

### Creating Objects

Objects can be created using methods of the generic function `drawGate` or via
`new("gate",`
`gateFun = ...., # function returning logical vector`
`colnames = .... # object of class character and length 2`
`logic = .... # object of class character`
`)`

### Slots

`name`:
  A character vector for the name of the `gate` object. You can reference the object by its name for subsequent operations (e.g. plotting).
`gateFun`:
  A function call together with necessary arguments to produce a logical vector when applied on the data.
`colnames`:
  The colnames of the data matrix to which the gating function is to be applied.
`logic`:
  A `character` object, either `&` or `|`. This specifies the logical operation that will be applied when combining the selection from the `gate` with other object of that class. See `link[prada]{gateSet}` for additional information on combining `gates`.
`type`:
  A `character` giving the type of the object. This is currently not used but might become important in the future.
`boundaries`:
  A `matrix` with two columns giving the boundaries of the gate in two dimensional space. Can be used to superimpose the gate boundaries on a plot using `lines()`.

### Methods

applyGate:
  `applyGate(x, data)`
  applies the gating of object `x` on data objects of class `cytoFrame` or `matrix`. In the former case `x` may be of class `gate`, `gateSet`, `character`, `numeric` or `logical`. See vignette for details.
show
  display summary.
names, names<-
  access and replace slot name.
as.gateSet
  Convert `gate` object to `gateSet` object
combineGates
  Combine multiple `gate` objects to one `gateSet` object
lines
  Draw the boundaries of the gate.

### Author(s)

Florian Hahne

### See Also

`cytoFrame`, `gateMatrix`, `gateSet`

### Examples

    sampdat <- readFCS(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                                   package="prada"))
    g1 <- new("gate", name="test1", gateFun=function(x)x[,"FSC-H"]<500, logic="&",
              colnames="FSC-H", type="misc")
    g1
    g2 <- new("gate", name="test2", gateFun=function(x)x[,"SSC-H"]>800, logic="&",
              colnames="SSC-H", type="misc")
    gs1 <- combineGates(g1,g2)
    gs2 <- as.gateSet(g2)
    names(g1)
    names(g1) <- "testName"
    applyGate(sampdat, g1)
    applyGate(exprs(sampdat), g2)
    gate(sampdat) <- g1
    applyGate(sampdat, 1)
    applyGate(sampdat, "testName")
    applyGate(sampdat, TRUE)

[Package prada version 1.10.1 Index]