read.series.FCS {rflowcyt} | R Documentation

## Reading a serie of raw binary Flow Cytometry Standard (FCS) files

### Description

Reads a serie of raw Flow Cytometry Standard (FCS) files and outputs several "FCS" R object.

### Usage

    read.series.FCS(fcsfiles,path=NULL,ext=NULL,...)

### Arguments

`fcsfiles` | names of the FCS files without any extension
`path` | a character vector of full path names; the default corresponds to the working directory `getwd`
`ext` | character string giving optional extension to be added to each file name
`...` | any other arguments are passed to `read.FCS`

### Details

This function read several FCS files by the means of the `read.FCS` function. Thus,this function can also checks if there are discrepancies between the data and the metadata in terms of range and size (MY.DEBUG=TRUE). If there is, then the data is re-read with different fcs.byte.size (1,2,4,8) and fcs.signed (TRUE, FALSE) combinations until there is no discrepancy between the data and the metadata. If there is still a discrepancy, then the routine is halted. Note: For FCS version 3.0 files, only the range of the data is checked against what is stated in the metadata because FCS version 3.0 files have extra elements that are read into the data.

### Value

No value is returned. However a series of "FCS" object are created on the current environment with names of the form filename. The files names are given by the elements of slides. Each object is composed of the same data and metadata return by the `read.FCS` function.

### Author(s)

N. Le Meur

### See Also

`read.FCS`, `summary`, `print`, `extractGatedData`, `addParameter`, `"[-methods"`, `"[[-methods"`, `fcs.type` `readCytoSet`

### Examples

     if (require(rfcdmin)) {

     ##obtaining the location of the fcs files in the data
      pathFiles<-system.file("bccrc", package="rfcdmin")
      drugFiles<-dir(pathFiles)

     ## reading in the FCS files
      drugData<-read.series.FCS(drugFiles,path=pathFiles,MY.DEBUG=FALSE)
      }

[Package rflowcyt version 1.6.0 Index]