fcs.type {rflowcyt} | R Documentation |
Objects providing parameters for the raw FCS file types
Description
The fcs.type
objects define the parameters needed for reading
in certain raw FCS files into R via the use of read.FCS
.
Currently this is just a script file defining certain fcs.type
objects, but ultimately this will be an environment. There are
certain read.FCS
parameters that are known to be
compatible for certain types of cytometers. The fcs.type
objects may be optionally used during the reading in of raw FCS files
into R and result in FCS R-objects (FCS objects).
Usage
fcs.type.default
Arguments
No arguments.
Details
A fcs.type is a list of the following:
- version
- raw FCS version number; value$=$"1.0" or "2.0" or "3.0"
- byte.size
- The byte size for the file (8 bits is one byte);
value=1 or 2 or 4, etc.
- signed
- boolean; If the data is signed; value$=$FALSE or TRUE
- endian
- The endian of the file depending on the endian of the
platform; Usually the value of endian is "big" (if both the file and
platform endian are "big") or "little" (if both the platform and the
file endian are "little") or "auto", then the read.FCS will
automatically detect the endian compatibility with the platform
system (See
readBin
for more details.)
The fcs.types are the following:
- 1. fcs.type.default
- a list of the following options and values:
- version
- "2.0"
- byte.size
- 2
- signed
- TRUE
- endian
- "auto"
- 2. fcs.type.cellquest.3.1.FACScan
- a list of the following options
and values:
- version
- "2.0"
- byte.size
- 1
- signed
- FALSE
- endian
- "auto"
- 3. fcs.type.LSR256
- a list of the following options
and values:
- version
- "2.0"
- byte.size
- 1
- signed
- FALSE
- endian
- "auto"
- 4. fcs.type.FACStar256
- a list of the following options
and values:
- version
- "2.0"
- byte.size
- 1
- signed
- FALSE
- endian
- "auto"
- 5. fcs.type.facscan256
- a list of the following options
and values:
- version
- "2.0"
- byte.size
- 1
- signed
- FALSE
- endian
- "auto"
- 6. fcs.type.cellquest.3.1.FACS.Vantage
- a list of the following
options and values:
- version
- "2.0"
- byte.size
- 2
- signed
- TRUE
- endian
- "auto"
- 7. fcs.type.cellquest.3.3
- a list of the following options and values:
- version
- "2.0"
- byte.size
- 2
- signed
- TRUE
- endian
- "auto"
- 8. fcs.type.LYSYS
- a list of the following options and values:
- version
- "2.0"
- byte.size
- 2
- signed
- TRUE
- endian
- "auto"
- 9. fcs.type.DiVa1024
- a list of the following options and values:
- version
- "2.0"
- byte.size
- 2
- signed
- TRUE
- endian
- "auto"
- 10. fcs.type.FACSCalibur1024
- a list of the following options and values:
- version
- "2.0"
- byte.size
- 2
- signed
- TRUE
- endian
- "auto"
- 11. fcs.type.LSR1024
- a list of the following options and values:
- version
- "2.0"
- byte.size
- 2
- signed
- TRUE
- endian
- "auto"
- 12. fcs.type.facscan1024
- a list of the following options and values:
- version
- "2.0"
- byte.size
- 2
- signed
- TRUE
- endian
- "auto"
Value
With the help of fcs.type, the raw FCS file will be read into a
FCS R object that can be implemented for further analysis in R.
Author(s)
A.J. Rossini and J.Y. Wan
References
Peter Rabinovitch
See Also
read.FCS
,
readBin
Examples
if (require(rfcdmin)) {
## obtaining the location of the fcs files in the data
get.path<-function(filename) {
datadir<-system.file("fcs", package="rfcdmin")
return(paste(datadir, filename, sep="/"))
}
FF256 <-read.FCS(get.path("facscan256.fcs"),
fcs.type=fcs.type.facscan256)
}
[Package
rflowcyt version 1.16.0
Index]