Question: clusterProfiler::enrichGO() is getting very slow
0
gravatar for sangram_keshari
10 days ago by
sangram_keshari190 wrote:

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.

go clusterprofiler R • 72 views
ADD COMMENTlink modified 10 days ago by jared.andrews072.7k • written 10 days ago by sangram_keshari190

Guangchuang Yu Any known issue with newer version or R?

ADD REPLYlink written 10 days ago by sangram_keshari190
0
gravatar for jared.andrews07
10 days ago by
jared.andrews072.7k
St. Louis, MO
jared.andrews072.7k wrote:

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.

ADD COMMENTlink written 10 days ago by jared.andrews072.7k
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