Running calculations in parallel

[y1zhou]

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!

[dkainer]

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.

[estayless]

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