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. Either 'prada' for cytoFrame objects or
'FCS' for rflowcyt 's FCS objects. |
... |
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
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.
An object of class cytoFrame
or
FCS
.
Wolfgang Huber http://www.ebi.ac.uk/huber, Florian Hahne
read.FCS
,
read.series.FCS
, readCytoSet
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)