Geno Ontology Analysis using gene symbol
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Entering edit mode
MOHAMMAD • 0
@MOHAMMAD-24781
Last seen 4 weeks ago

My Genome wide annotation package does not contain a column for gene_id or ENTREZID

enter image description here

I was trying to use the following function to get the gene ontology :

ggo <- groupGO(gene = gene_0.1,
                   OrgDb = org.Pf.plasmo.db,
                   ont = "CC",
                   level = 3,
                   readable = TRUE)

i got the following error

Error in .getDBLoc(x, cols[i], value = value) : 'col' value 'ENTREZID' is not defined

is there any alternative tool/package that utilizes "SYMBOL" instead

thank you in advance

GO.db Annotation Clusterprofile GeneOntology • 103 views
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2
Entering edit mode
Basti ▴ 70
@7d45153c
Last seen 10 hours ago
France

I think you have to add a keytype to your query :

ggo <- groupGO(gene = gene_0.1,
                   OrgDb = org.Pf.plasmo.db, keytype="SYMBOL",
                   ont = "CC",
                   level = 3)
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