outFCS {CATALYST} | R Documentation

## Write population-wise FCS files

### Description

Writes an FCS file for each sample from a dbFrame.

### Usage

    outFCS(x, y, out_path = tempdir(), ...)

    ## S4 method for signature 'dbFrame,flowFrame'
    outFCS(x, y, out_path = tempdir(),
      out_nms = NULL, verbose = TRUE)

### Arguments

`x` | a `dbFrame`.
`y` | a `flowFrame` containing the original measurement and meta data.
`out_path` | character string. Specifies in which location output files are to be generated.
`...` | optional arguments.
`out_nms` | an optional character string. Either the name of a 2 column CSV table with sample IDs and desired output file names, or a vector of length `nrow(bc_key(x))` ordered as the samples in the barcoding scheme. If NULL (default), sample IDs will be used as file names.
`verbose` | if TRUE (default), a warning is given about populations for which no FCS files have been generated.

### Details

Creates a separate FCS file for each barcode population. If `out_nms` is NULL (the default), files will be named after the barcode population's ID in the `bc_key` slot of the input `dbFrame`; unassigned events will be written to "unassigned.fcs", and no output is generated for populations with less than 10 event assignments.

### Value

a character of the output path.

### Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

### Examples

    data(sample_ff, sample_key)
    re <- assignPrelim(x = sample_ff, y = sample_key)
    re <- estCutoffs(x = re)
    re <- applyCutoffs(x = re)
    outFCS(x = re, y = sample_ff)

[Package CATALYST version 1.8.7 Index]