Question

compute similarities of GOTerms with GOSim in non-human species

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monifass ▴ 10

@monifass-18039

Last seen 5.5 years ago

Hi everyone,

I am intending to use GOSim to calculate similarities between different GO Terms obtained by Enrichment Analysis of expression data in a plant species. Therefore, I want to use specifically the 'getTermSim' function. However, since this function uses by default the human database, I want to change this and use the Arabidopsis thaliana database (org.At.tair.db) instead. As far as I understand, I have to compute first the ICs for this database from scratch, but I am having some trouble understanding how to achieve this, probably due to lack of experience. Can someone give me some guidance as how to use GOSim with another (non-human) species? Is there documentation I have missed?

Thank you!

GOSim • 821 views

ADD COMMENT • link updated 5.5 years ago by Lluís Revilla Sancho ▴ 730 • written 5.5 years ago by monifass ▴ 10

score 2 · Accepted Answer · 2018-10-27

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Lluís Revilla Sancho ▴ 730

@lluis-revilla-sancho

Last seen 3 days ago

European Union

To build the IC you need to tho this:

library(GOSemSim)
GOMF <- godata('org.At.tair.db', ont="MF")

And use this GOMF object to calculate the similarity between molecular function terms of Arabidopsis thaliana. You can find this information under Supported organisms' section of the vignette.

ADD COMMENT • link 5.5 years ago Lluís Revilla Sancho ▴ 730

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I thought the GOSemSim package don't support many species, that's why I wanted to use the GOSim package, but now I have a good solution. Thank you!! This worked for me!

ADD REPLY • link 5.5 years ago monifass ▴ 10