readFCS {prada} | R Documentation |
Read one or several FCS files: Data File Standard for Flow Cytometry
read.fcs(filename=NULL, objectModel="prada", ...) readFCS(filename)
filename |
Character of length 1: filename |
objectModel |
Character of length 1: the object model to use for the
output. Curently only 'prada' for |
... |
Arguments that get passed on to higher-level import functions. |
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.
An object of class cytoFrame
.
Wolfgang Huber http://www.ebi.ac.uk/huber, Florian Hahne
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)