convertS3toS4 {rflowcyt}R Documentation

Converts S3 class FCS object to S4 class FCS object

Description

This function will update any S3 class FCS object to S4 class.

Usage

convertS3toS4(S3file, myFCSobj.name = "", fileName = "")

Arguments

S3file S3 Class FCS object location and filename
myFCSobj.name character string indicating the FCS object name
fileName character string indicating the file name of the binary raw FCS data, from which the FCS object originates and which is read by read.FCS

Details

The FCS object is obtained as the result of read.FCS which has been currently updated to output FCS objects as class S4 instead of S3.

Value

A Class S4 FCS object with the following slots:

data matrix of the data, where the rows are the cells/observations and the columns are the different fluoroescence measurements
metadata of class FCSmetadata with the following slots:
mode
the mode of the raw binary file

size
numeric value describing the total number of rows or observations/cells

nparam
numeric value describing the number of columns or parameters

shortnames
a vector of the short names of the column variables of the data

longnames
a vector of the long names of the column variables of the data

paramranges
the vector of corresponding ranges or maximum values for each column variable

filename
character string of the name of the raw data file from which the object originates

objectname
character string of the name of the FCS S4 object

original
Boolean value indicating whether the data is the original

fcsinfo
list of other parameters

Author(s)

A.J. Rossini and J.Y. Wan

See Also

read.FCS, FCS

Examples

  if (require(rfcdmin)){

     ## if previously read-in as S3 FCS object
     facscan256.fcs<- paste(system.file("fcs", package="rfcdmin"),
                              "facscan256.fcs",
                              sep="/")

     ## reading in the FCS files
     FCSobj.S3<-read.FCS(facscan256.fcs, UseS3=TRUE)

     ## convert to S4 FCS

     FCSobj.S4<- convertS3toS4(FCSobj.S3,
                               myFCSobj.name="FCSobj.S4",
                               fileName=facscan256.fcs)
  }

[Package rflowcyt version 1.4.0 Index]