R-Rename FCS

This short R script takes an input folder of FCS files and configurably does the following:

• Unflips width and height axes to account for BD FACSDiva's improper flipping of these parameters when exporting an entire experiment
• Renames a map of parameters so they can be reflected of the actual fluorophore names and appropriately updates the compensation matrix
• Renames the FCS $FIL keyword to the given file's name

Prerequisites

Install R and the flowCore package:

R

Install R via Winget:

winget install -e --id RProject.R

Then install the flowCore package. Run:

R.exe

FlowCore

This will obtain an R prompt. Then:

install.packages('jsonlite', dependencies=TRUE, repos='http://cran.rstudio.com/')
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("flowCore")

Usage

Create a config.json file in the same folder as the script. For example:

{
    "parameter_replacements": {
        "BV421-A": "DAPI-eF450-A",
        "APC-A": "eF660-A"
    },
    "flip_width_height": true
}

Then via Powershell in the directory containing index.r and the data folder for FCS files:

Rscript index.r