write.flowSet: Write an FCS file
In flowCore: flowCore: Basic structures for flow cytometry data

Description Usage Arguments Details Value Author(s) See Also Examples

Write FCS file for each flowFrame in a flowSet

1	write.flowSet(x, outdir=identifier(x), filename, ...)

`x`	A `flowSet`.
`outdir`	A character scalar giving the output directory. As the default, the output of `identifier(x)` is used.
`filename`	A character scalar or vector giving the output file names. By default, the function will use the identifiers of the individual `flowFrames` as the file name, potentially adding the `.fcs` suffix unless a file extension is already present. Alternatively, one can supply either a character scalar, in which case the prefix `i_` is appended (`i` being an integer in `seq_len(length(x))`), or a character vector of the same length as the `flowSet x`.
`...`	Further arguments that are passed on to `write.FCS`.

The function write.flowSet creates FCS 3.0 standard file for all flowFrames in an object of class flowSet. In addition, it will write the content of the phenoData slot in the ASCII file "annotation.txt". This file can subsequently be used to reconstruct the whole flowSet using the read.flowSet function, e.g.:

read.flowSet(path=outdir, phenoData="annotation.txt"

The function uses write.FCS for the actual writing of the FCS files.

A character vector of the output directory.

F. Hahne

link[flowCore]{write.FCS}

## sample data
data(GvHD)
foo <- GvHD[1:5]
outDir <- file.path(tempdir(), "foo")

## now write out into  files
write.flowSet(foo, outDir)
dir(outDir)

## and read back in
bar <- read.flowSet(path=outDir, phenoData="annotation.txt")