cytoFrame-class {prada} | R Documentation

## 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy

### Description

This class represents the data contained in a FCS 3.0 file or similar data structures.

### Details

Although objects of class `cytoFrame` can be used to hold arbitrary data of cell populations, the main focus lies on flow-cytometry data.

FCS 3.0 is the Data File Standard for Flow Cytometry, Version FCS3.0. See the vignette of this package for additional information on using the object system for handling of flow-cytometry data.

### Creating Objects

Objects can be created using
`new('cytoFrame,`
`exprs = ...., # Object of class matrix`
`description = .... # Object of class character`
`)`
or the function `readFCS`.

### Slots

`exprs`:
  Object of class `matrix` containing the measured intensities. Rows correspond to cells, columns to the different channels. The `colnames` attribute of the matrix is supposed to hold the names or identifiers for the channels. The `rownames` attribute would usually not be set.
`description`:
  A named character vector containing the experiment description as key-value pairs.
`well`:
  A single integer vector giving the position of the well on a microtitre plate. This only applies when using the object within a `cytoSet` collection and will usually be filled in by the function `readCytoSet`.
`gate`:
  An object of class `gateSet`. This object can be used to select defined subsets of the data, a process referred to as `gating` in the analysis of flow-cytometry data.

### Methods

[
  subsetting. Returns an object of class `cytoFrame`. The subsetting is applied to the `exprs` slot, while the `description` slot is unchanged.
exprs, exprs<-
  extract or replace the intensities.
description, description<-
  extract or replace the description.
show
  display summary.
plot
  scatterplot for `cytoFrame` objects. The additional argument `gate` can be used to plot subsets of the data defined by either an object of class `gate` or by a character vector giving the name of one of the gates in the list.
gate,gate<-
  extract or replace the list of gates.
ncol,nrow
  extract the dimensions of the data matrix.
appendGate
  Append a gate or gateSet to the gate slot.
drawGate
  Create an object of class `gate` or `gateSet` based on a selection made from the data. See `gateMatrix` for further details.
hist
  Draw a histogram of the data

### Author(s)

Florian Hahne, Wolfgang Huber

### See Also

`readFCS`, `cytoSet`, `gate`, `gateSet`, `gateMatrix`

### Examples

    intens <- matrix(runif(100), ncol=4)
    colnames(intens) <- c("FL1-H", "FL2-H", "FL3-H", "FL4-H")

    a <- new("cytoFrame",
              exprs=intens,
              description=c(name="example data", date=date()))

    description(a)
    dim(exprs(a))

    a[1:3, -4]

    plot(a)
    ## Not run:
    g1 <- drawGate(a, name="Gate1")
    ## End(Not run)

[Package prada version 1.10.1 Index]