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]