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 1.10.3 Index]