read.FCS {flowCore} | R Documentation |
Read Data File Standard for Flow Cytometry
read.FCS(filename, transformation = "linearize", debug = FALSE, alter.names=FALSE, column.pattern=NULL)
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. |
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.
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.
F. Hahne, N.Le Meur
link[flowCore]{read.flowSet}
samp <- read.FCS(system.file("extdata", "0877408774.B08", package="flowCore"), transformation="linearize") exprs(samp[1:3,]) description(samp)[3:6] class(samp)