GO enrichment for non-model plant species
0
0
Entering edit mode
@sandeepamberkar18-21432
Last seen 14 months ago
Rothamsted Research UK

Hello,

Has anyone done an enrichment analysis for non-model plant species such as Wheat (Triticum aestivum). As a first step, I generated a gene-GO-GOdescription mapping as fetched from Ensembl Plants, which looks something like this:

              GeneID      GO-ID                                       GO-Description

TraesCS3A02G154800 GO:0047617                          acyl-CoA hydrolase activity
 TraesCS2B02G516800 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
 TraesCS2B02G516800 GO:0005975                       carbohydrate metabolic process
 TraesCS2B02G516800 GO:0016787                                   hydrolase activity
 TraesCS2B02G516800 GO:0016798         hydrolase activity, acting on glycosyl bonds
 TraesCS2B02G516800 GO:0008152                                    metabolic process

I'm trying to generate an MSigDB type gmt file from this table, which can then be used as input for the clusterProfiler function enricher.

I get duplicates found error which is why I can't proceed any further with an enrichment analysis.

Any body has any nifty solution, please do share.

With thanks.

Best, Sandeep

clusterProfiler GSEABase GMTfiles • 502 views
ADD COMMENT
0
Entering edit mode

How did you create the gmt file? Did you try to create a GeneSetCollection for clusterProfiler (this way you wouldn't need to create a gmt file)?

ADD REPLY
0
Entering edit mode

No, I didn't create a GeneSetCollection object. How could that be passed to enricher function?

ADD REPLY
0
Entering edit mode

I think that you can convert it to a list, or it is already accepted, but check the vignette and the manuals

ADD REPLY

Login before adding your answer.

Traffic: 294 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