Mapping IDs to systematic names (GOSim, setevidencelevel() )
0
0
Entering edit mode
16 months ago

Hi,

I want to use the GoSim package to calculate the IC similarity. I'm trying to set the parameters of setEvidenceLevel(), but wrong. What mapping to use for the gomap parameter, please? So my problem is with mapping IDs to systematic names. I'm a computer scientist, not a bioinformatician, so I apologize for the possibly stupid question.

I use the same vector as used here: Translating gene names to entrez id's

genes <- c('BRCA1', 'BRCA2', 'BRCC3', 'ATM', 'TP53')
library(org.Hs.eg.db) 
library(GOSim) 
setEvidenceLevel(evidences =  "all", organism=org.Hs.egORGANISM, gomap=org.Hs.egGO)  
setOntology("BP") 
getGOInfo('BRCA1')

I always get an error :

„getGOInfo("BRCA1") : No GO information available for these genes!“

The same holds for

 setEvidenceLevel(evidences =  "all", organism=org.Hs.egORGANISM, gomap=org.Hs.egSYMBOL)

Select() works, see: Translating gene names to entrez id's

I am trying to do it in the same manner as recommended for Yeast here https://support.bioconductor.org/p/45669/#93785 which works for me.

GOSim • 282 views
ADD COMMENT

Login before adding your answer.

Traffic: 2367 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