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 1.10.1 Index]