Geno Ontology Analysis using gene symbol
1
0
Entering edit mode
MOHAMMAD • 0
@MOHAMMAD-24781
Last seen 3.6 years 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 • 1.0k views
ADD COMMENT
2
Entering edit mode
Basti ▴ 780
@7d45153c
Last seen 1 hour 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)
ADD COMMENT

Login before adding your answer.

Traffic: 923 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6