updated GO dataframe in R
2
0
Entering edit mode
2.1 years ago
lessismore ★ 1.3k

Dear all,

I'm performing GO analyses with R I'd need to get the most updated gene ontology list of terms as a dataframe with ID, ontology (BP, CC, MF), description columns. Does anyone know the best way to do this, or a package having it as a dataset by default? or a way to convert an obo file from here http://geneontology.org/docs/download-ontology/ into a dataframe?

thanks in advance

r.gene ontology • 1.1k views
ADD COMMENT
0
Entering edit mode
2.1 years ago
jv ★ 1.8k

I like using the Org.XX.eg.db annotation packages from Bioconductor (where XX is an abbreviation for your model organism, e.g. the Homo sapiens annotation package is named Org.Hs.eg.db).

There's a package available for many of the common eukaryotic model organisms - go to https://bioconductor.org/packages/3.14/data/annotation/ and search in the page for "Org" and you'll find a list of different options.

ADD COMMENT
0
Entering edit mode

Thanks! This is a very cool way and I know it, but unfortunately I need to build my own package (with annotationforge package) as I'm working with a non model organism. The GO annotation I've found to build it doesn't display the ontology code (BP, CC, MF) but just the GO id and its description. So I was wandering the fastest way to add this column to my GO annotation dataframe.

ADD REPLY
0
Entering edit mode
2.1 years ago
EagleEye 7.5k

GeneSCF (Gene Set Clustering based on Functional annotation): Most up-to-date and realtime information based gene enrichment analysis.

Updating GeneSCF with complete geneontology database or download the terms as simple text file for human

./geneSCF-master-vx.x/prepare_database -db=GO_all -org=goa_human

Note: Specific dabases can be also updated using 'GO_BP', 'GO_MF' and 'GO_CC'. The above command downloads complete geneontology ('GO_all') with corresponding genes per GO term as simple text file in following location, 'geneSCF-master-vx.x/class/lib/db/goa_human/'.

ADD COMMENT

Login before adding your answer.

Traffic: 2417 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