Extract geneID following GO enrichment analysis

Question

[hellokwmin]

Hello,

I have performed GO analysis using enrichGO function provided from Clusterprofiler package used in R.

This is my code I used for that as follows:

ego = enrichGO(gene = df$REFSEQ,
               OrgDb = "org.At.tair.db",
               keyType = "TAIR",
               ont = "ALL",
               pAdjustMethod = "BH",
               pvalueCutoff = 0.05,
               qvalueCutoff = 0.05,
               readable = TRUE)

After running this code, I have obtained the results consisted of ONTOLOGY, GOID, DESCRIPTION, GENERATIO, BGRATIO, PVALUE, P.ADJUST, QVALUE AND GENEID; i attached example as below:

My question is in the geneID column, there are lists of geneID belonging to each GO id. But, some gene IDs are makred as NA. probably, cannot find a proper geneID or not yet annotated in arabidopsis database used in my code. But, I would like to know at least REFSEQ number which I inserted into my code. In other words, which REFSEQ is finally makred as NA that is belong to each GO ID? Is there any ways to know that?

[Nitin Narwade]

I think, you are getting these NA values in your output because readable=TRUE.

As per this description,

Gene IDs can be mapped to gene Symbols by using the parameter readable=TRUE or setReadable() function.

Your gene ids are getting converted to gene symbols in that case some of your ids does not have gene names.

Try to set it FALSE and you should get gene ids in your output.

Regards,

Nitin N.

[hellokwmin]

Thank you so much.