read.FCS {flowCore}R Documentation

Read an FCS file

Description

Read Data File Standard for Flow Cytometry

Usage

   read.FCS(filename, transformation = "linearize", debug = FALSE, alter.names=FALSE, column.pattern=NULL)

Arguments

filename Character of length 1: filename
transformation An character string that defines the type of transformation. Valid values are linearize (default) or standardize.The former applies the appropriate power transform to the data while the latter scales all columns to [0,1] as in the FCS4 specification. A logical can also be used: TRUE is equal to linearize and FALSE correponds to no transformation.
debug boolean indicating whether or not to print the debugging statements, default is TRUE
alter.names boolean indicating whether or not we should rename the columns to valid R names using make.names. The default is FALSE.
column.pattern An optional regular expression defining parameters we should keep when loading the file. The default is NULL.

Details

The function read.FCS works with the output of the FACS machine software from a number of vendors (FCS 2.0, FCS 3.0 and List Mode Data LMD). 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 function is an object of class flowFrame.

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 flowFrame that contains the data in the exprs slot, the parameters monitored in the parameters slot and the keywords and value saved in the header of the FCS file.

Author(s)

F. Hahne, N.Le Meur

See Also

link[flowCore]{read.flowSet}

Examples

samp <- read.FCS(system.file("extdata",
   "0877408774.B08", package="flowCore"), transformation="linearize")
exprs(samp[1:3,])
description(samp)[3:6]
class(samp)

[Package flowCore version 1.0.2 Index]