Parallelize 'DESeq2' functions

Henrik Bengtsson

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The futurize package allows you to easily turn sequential code into parallel code by piping the sequential code to the futurize() function. Easy!

TL;DR

library(futurize)
plan(multisession)
library(DESeq2)

dds <- DESeqDataSetFromMatrix(countData, colData, design = ~ condition)
dds <- DESeq(dds) |> futurize()

Introduction

This vignette demonstrates how to use this approach to parallelize the DESeq2 DESeq() function.

The DESeq2 Bioconductor package provides methods to test for differential expression in RNA-seq data. The main function DESeq() runs a pipeline of gene-wise dispersion estimation, fitting, and statistical testing, which can be parallelized across genes.

Example: Running DESeq() in parallel

The DESeq() function performs the full differential expression analysis:

library(DESeq2)

# Simulate data
n_genes <- 100L
n_samples <- 8L
counts <- matrix(
  as.integer(runif(n_genes * n_samples, min = 0, max = 1000)),
  nrow = n_genes,
  ncol = n_samples,
  dimnames = list(
    paste0("gene", seq_len(n_genes)),
    paste0("sample", seq_len(n_samples))
  )
)
 
col_data <- data.frame(
  condition = factor(rep(c("control", "treated"), each = n_samples / 2L)),
  row.names = colnames(counts)
)

dds <- DESeqDataSetFromMatrix(
  countData = counts,
  colData = col_data,
  design = ~ condition
)

dds <- DESeq(dds)
res <- results(dds)

Here DESeq() runs sequentially, but we can easily make it run in parallel by piping to futurize():

library(futurize)

dds <- DESeq(dds) |> futurize()
res <- results(dds)

This will distribute the work across the available parallel workers, given that we have set up parallel workers, e.g.

plan(multisession)

The built-in multisession backend parallelizes on your local computer and works on all operating systems. There are other parallel backends to choose from, including alternatives to parallelize locally as well as distributed across remote machines, e.g.

plan(future.mirai::mirai_multisession)

and

plan(future.batchtools::batchtools_slurm)

Supported Functions

The following DESeq2 functions are supported by futurize():

• DESeq()
• lfcShrink()
• results()