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 ```r library(futurize) plan(multisession) library(fgsea) res <- fgsea(pathways, stats) |> futurize() ``` # Introduction This vignette demonstrates how to use this approach to parallelize the **[fgsea]** functions. The **[fgsea]** Bioconductor package implements fast preranked gene set enrichment analysis (GSEA). The main functions `fgsea()`, `fgseaMultilevel()`, and `fgseaSimple()` perform permutation-based enrichment testing, which can be parallelized across gene sets. ## Example: Running fgseaSimple() in parallel The `fgseaSimple()` function performs permutation-based gene set enrichment analysis: ```r library(fgsea) # Create example data set.seed(42) n_genes <- 1000L stats <- rnorm(n_genes) names(stats) <- paste0("gene", seq_len(n_genes)) pathways <- list( pathway1 = paste0("gene", sample(n_genes, 50L)), pathway2 = paste0("gene", sample(n_genes, 100L)), pathway3 = paste0("gene", sample(n_genes, 150L)) ) res <- fgseaSimple(pathways, stats, nperm = 10000) ``` Here `fgseaSimple()` runs sequentially, but we can easily make it run in parallel by piping to `futurize()`: ```r library(futurize) res <- fgseaSimple(pathways, stats, nperm = 10000) |> futurize() ``` This will distribute the work across the available parallel workers, given that we have set up parallel workers, e.g. ```r 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. ```r plan(future.mirai::mirai_multisession) ``` and ```r plan(future.batchtools::batchtools_slurm) ``` # Supported Functions The following **fgsea** functions are supported by `futurize()`: * `fgsea()` * `fgseaMultilevel()` * `fgseaSimple()` * `fgseaLabel()` * `geseca()` * `gesecaSimple()` * `collapsePathwaysGeseca()` [fgsea]: https://bioconductor.org/packages/fgsea/ [other parallel backends]: https://www.futureverse.org/backends.html