Running calculations in parallel

Open y1zhou opened this issue 5 years ago • 2 comments

Is it possible to replace the sapply and apply's in the code with BiocParallel::bplapply? For example mclusterSim becomes really slow when the number of clusters / the size of the clusters gets large. Thanks for the good work!

Aug 24 '20 04:08 y1zhou

i had the same issue with mgeneSim for a large number of genes. I modified it with a parallelised outer for-loop using foreach and found that for thousands of genes it kept the run-time down considerably.

I think there are a lot of points in the GOSemSim code that could benefit from simple parallelising.

Dec 04 '20 15:12 dkainer

@dkainer Could you share your solution for mgeneSim please? I am trying to improve the same function.

Dec 14 '20 00:12 estayless