Parallelize 'sva' 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(sva)

adjusted <- ComBat(dat = dat, batch = batch) |> futurize()

Introduction

This vignette demonstrates how to use this approach to parallelize the sva functions.

The sva Bioconductor package provides functions for removing batch effects and other unwanted variation in high-throughput experiments. The ComBat() function is a widely used method for batch effect correction using an empirical Bayes framework. It supports parallelization via BiocParallel’s BPPARAM argument.

Example: Running ComBat() in parallel

The ComBat() function adjusts for known batch effects in microarray or RNA-seq data:

library(sva)

# Create example data with batch effect
set.seed(42)
n_genes <- 200L
n_samples <- 40L
dat <- matrix(rnorm(n_genes * n_samples), nrow = n_genes, ncol = n_samples)
rownames(dat) <- paste0("gene", seq_len(n_genes))
colnames(dat) <- paste0("sample", seq_len(n_samples))

batch <- rep(c(1, 2), each = n_samples / 2L)
dat[, batch == 2] <- dat[, batch == 2] + 2

adjusted <- ComBat(dat = dat, batch = batch)

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

library(futurize)

adjusted <- ComBat(dat = dat, batch = batch) |> futurize()

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)

Using ComBat() with a model matrix

You can also include a model matrix for biological covariates of interest, which will be protected during batch correction:

mod <- model.matrix(~ group)
adjusted <- ComBat(dat = dat, batch = batch, mod = mod) |> futurize()

Supported Functions

The following sva functions are supported by futurize():

• ComBat()
• read.degradation.matrix()