FCS-to-CSV v2.0.R

# FCS to CSV
    # Converting .fcs file data into an .csv file
    # Thomas Ashhurst (2017-09-13) [github.com/sydneycytometry]
    # *adapted from [https://gist.github.com/yannabraham/c1f9de9b23fb94105ca5]

# Code refactoring by Christian Rickert (2022-03-31)

# Install required packages
if(!requireNamespace("BiocManager", quietly = TRUE)) {install.packages("BiocManager", quiet = TRUE)}
if(!require('flowCore')) {BiocManager::install("flowCore", update = FALSE)}
if(!require('Biobase')) {BiocManager::install("Biobase", update = FALSE)}
if(!require('data.table')) {install.packages('data.table')}
if(!require('rstudioapi')) {install.packages('rstudioapi')}

# Load packages
library('flowCore')
library('Biobase')
library('data.table')
library('rstudioapi')

# Set input and output variables
currentFolder <- dirname(rstudioapi::getSourceEditorContext()$path)  # script location
importFolder <- file.path(currentFolder, "import", fsep = .Platform$file.sep)  # relative path
exportFolder <- file.path(currentFolder, "export", fsep = .Platform$file.sep)
filePattern  <- "\\.fcs$"  # match file extension (case-insensitive)

# Set up working directories
if (!file.exists(importFolder)) {dir.create(importFolder)}
print(paste("Input folder: ", importFolder))
if (!file.exists(exportFolder)) {dir.create(exportFolder)}
print(paste("Export folder: ", exportFolder))

# Get list of input files
FileNames <- list.files(path = importFolder, pattern = filePattern, ignore.case = TRUE)

# Read data from CSV and write FCS data
for (FileName in FileNames) {
  print(FileName)

  setwd(importFolder)
  FileData <- exprs(read.FCS(FileName, transformation = FALSE))

  setwd(exportFolder)
  write.csv(FileData, paste0(FileName, ".csv"))
}