readFCS: Read an FCS file

Description

Read one or several FCS files: Data File Standard for Flow Cytometry

Usage

read.fcs(filename=NULL, objectModel="prada", ...) readFCS(filename)

Arguments

filename

Character of length 1: filename

objectModel

Character of length 1: the object model to use for the output. Curently only 'prada' for cytoFrame objects is supported.

...

Arguments that get passed on to higher-level import functions.

Value

cytoFrame.

Details

The function readFCS works with the output of the FACS machine software from a number of vendors. However, the FCS 3.0 standard includes some options that are not yet implemented in this function. If you need extensions, please let me know. The output of the fucntion is an object of class cytoFrame.

read.fcs is a wrapper function that allows the user to specify the class of the output. The purpose of the function is to standardize the way flow cytometry data is imported into R using the prada package. If the filename argument to read.fcs is a character vector of length > 1, multiple FCS files can be imported. Please see the documentation for readCytoSet for alternatives ways to import multiple FCS files and for more details on the higher-level import function.

For specifications of FCS 3.0 see http://www.isac-net.org and the file ../doc/fcs3.html in the doc directory of the package.

Examples

Run this code

sampdat <- readFCS(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                               package="prada"))
files <- dir(system.file("extdata", package="prada"),
             pattern="[A-H][0-9][0-9]")
sampdat2 <- read.fcs(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                               package="prada"))
sampdat3 <- read.fcs(files, path=system.file("extdata", package="prada"))
sampdat
exprs(sampdat[1:3,])
description(sampdat)[3:6]
class(sampdat3)