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

Description

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

Details

FCS 3.0 is the Data File Standard for Flow Cytometry, Version FCS3.0.

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.

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.

Author(s)

Wolfgang Huber

See Also

readFCS, cytoSet-class

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)