clusterProfiler::enrichGO() is getting very slow

Question

[sangram_keshari]

I am trying to run clusterProfiler::enrichGO() for 10 Human Ensemble IDs but its getting very slow. Sometimes it takes 15 minutes and other time more than half an hour. Also, its taking all the available RAM in a 8GB machine.

My R session dosn't have any other loaded package or objects.

I am using r=3.5 and clusterprofiler=3.10.1

Similar issue reported earlier: https://github.com/GuangchuangYu/clusterProfiler/issues/155

Even from what I remember it wasn't taking this long when I run few months back.

Any help or an alternatives which support as many organisms internally (with OrgDB) like this package does.

[sangram_keshari]

Guangchuang Yu Any known issue with newer version or R?

[Guangchuang Yu]

we optimized the code and now it take less memory and run faster in clusterProfiler 4.0

Answer 1

[jared.andrews07]

Swap your identifiers to Entrez IDs. I don't know why, but clusterProfiler doesn't love other types of identifiers. I ran into the same issues trying to use both gene symbols and Ensemble IDs, but swapping them to Entrez IDs fixed it.

Answer 2

[garcesj]

I faceted the same issue and I ran out of patience... maybe enrichR could helps you. Bests!