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Question: How to arrive at an optimal value for attribute level in groupGO or enrichGO in clusterprofiler
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gravatar for saadmurtazakhan
6 months ago by
United States
saadmurtazakhan10 wrote:

Hi ,

I am trying to use your R package clusterprofiler. My question is with regards to groupGO function. I was wondering what would be a good value to use for "level" attribute in the function. Or is there a way to arrive at the most optimal value for the attribute "level".


thanks 

ggo <- groupGO(gene = as.character(subset_aggdf$annot.gene_id),
OrgDb = org.Mm.eg.db,
ont = "MF",
level = 10,
readable = TRUE)

ADD COMMENTlink modified 6 months ago by Guangchuang Yu1.1k • written 6 months ago by saadmurtazakhan10
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gravatar for Guangchuang Yu
6 months ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

I would recommend you using enrichGO function to test whether your genes are significantly related to which GO terms.

ADD COMMENTlink written 6 months ago by Guangchuang Yu1.1k
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