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 1.14.0 Index]