Possible to use parallelization to speed up non-parametric estimation in R?

Jfortin1 / ComBatHarmonization

Harmonization of multi-site imaging data with ComBat

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Possible to use parallelization to speed up non-parametric estimation in R? #27

Closed dpagliaccio closed 3 years ago

dpagliaccio commented 3 years ago

Hi I am testing out neuroCombat to harmonize fMRI data across two sites. The parametric version works great even on a larger number of input features. But it takes an exceedingly long time to run the non-parametric version with thousands of features. I was wondering if it would be possible to use parallel processing to speed this up? Particularly the getEbEstimators helper function for "Finding non-parametric adjustments" Thanks!

Jfortin1 commented 3 years ago

Thank you for the suggestion. BiocParallel options now added to v 1.0.7(https://github.com/Jfortin1/ComBatHarmonization/commit/145bce4075c84e3d99358061928f4fafb4db70ac)