readFCS {prada}R Documentation

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. Either 'prada' for cytoFrame objects or 'FCS' for rflowcyt's FCS objects.
... Arguments that get passed on to higher-level import functions.

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 or rflowcyt packages. 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 and read.series.FCS for alternatives ways to import multiple FCS files and for more details on the higher-level import function.

Be aware that rflowcyt needs to be installed when the function is run with argument objectModel="FCS".

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.

Value

An object of class cytoFrame or FCS.

Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber, Florian Hahne

See Also

read.FCS, read.series.FCS, readCytoSet

Examples

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)

[Package prada version 1.14.0 Index]