flowCoreUtils

flowCoreUtils provides utilities and sometimes faster replacements for the Bioconductor flowCore package.

Features

• Automatic Overload: Once loaded, it replaces flowCore::read.FCS with a faster version for large files.
• Smart Fallback: Automatically reverts to the original flowCore logic for edge cases or specific file types.
• Toggleable: Switch back to the original implementation at any time.

Installation

Binary installation for Windows

Find the release to install at https://github.com/i-cyto/flowCoreUtils/releases. Windows release have an extension ".zip". The example below uses the URL of the first release.

binary_url <- "https://github.com/i-cyto/flowCoreUtils/releases/download/v0.0.0.9000/flowCoreUtils_0.0.0.9000.zip"
install.packages(binary_url, repos = NULL, type = "win.binary")

Source installation with compilation (Rtools needed for Windows)

remotes::install_github("i-cyto/flowCoreUtils")

Usage

Simply loading the library activates the optimization:

library(flowCore)
library(flowCoreUtils)

# Check overload
environment(flowCore::read.FCS)  # should point to flowCoreUtils

# This now uses the optimized version if the "specific case" is met
data <- read.FCS("large_sample.fcs")

# Revert to standard flowCore behavior manually:
restore_original_read.FCS()
environment(flowCore::read.FCS)  # should point to flowCore

# Turn it back on:
enable_fast_read()

⚠️Warning on Namespace Injection

This package uses assignInNamespace to ensure that even internal calls from other packages benefit from the speed increase. This affects the global R session. Use at your own risks!