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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!
library(futurize)
plan(multisession)
library(SingleCellExperiment)
library(scuttle)
result <- applySCE(sce, perFeatureQCMetrics) |> futurize()
This vignette demonstrates how to use this approach to parallelize the SingleCellExperiment functions.
The SingleCellExperiment Bioconductor package defines the
SingleCellExperiment class for storing single-cell genomics data,
including alternative experiments (e.g. spike-in transcripts, antibody
tags). The applySCE() function applies a given function to the main
experiment and each alternative experiment, passing additional
arguments such as BPPARAM via ... to enable parallelization of
the applied function.
The applySCE() function applies a function across the main
experiment and its alternative experiments:
library(SingleCellExperiment)
library(scuttle)
# Simulate data
sce <- mockSCE()
result <- applySCE(sce, perFeatureQCMetrics)
Here applySCE() runs perFeatureQCMetrics() from the scuttle
package sequentially on each experiment, but we can easily make it run
in parallel by piping to futurize():
library(futurize)
result <- applySCE(sce, perFeatureQCMetrics) |> futurize()
It is actually not SingleCellExperiment::applySCE() that
orchestrates the parallelization, but scuttle::perFeatureQCMetrics(),
which hands of the parallelization to BiocParallel which in turn
hands it of to futureverse.
The above 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)
The following SingleCellExperiment functions are supported by futurize():
applySCE()