GO redundancy reduction

Question

[lessismore]

Dear all,

i have a plain text file with a list of GO that were significant in my enrichment analysis and i would like to reduce its redundancy (just like REVIGO is doing). Could you please suggest a way to do this? Preferably an R package. Output should be another plain text file.

Thanks in advance

[lieven.sterck]

no idea how (or if) you do this with R but you could map them to GOslim ?

[AK]

You could use goSlim from GSEABase.

[Friederike]

why is REVIGO not up for the job?

[lessismore]

Because i'd like to automate it and didn't find script to do it with REVIGO.

[Friederike]

Ah, that's a different question then! :) Why don't you re-phrase your question to something like "How can I automate REVIGO" and I'll point you to a script that does it.

Answer 1

[Friederike]

For automating REVIGO submissions, you can use this python script (which I originally found on biostars, too, I believe). I don't fully remember which changes I made, but you can see my version here.

I would use it like this in R (pseudo-code! don't use as is):

fname_out_revigo <- paste0(out_path, "REVIGO_results")
fname_out2 <- paste0(fname_out_revigo, ".R")
py_script <- "download_revigo_improved.py"

## submit to REVIGO using the python script
system(paste(python, py_script, GO_term_list, fname_out_revigo), wait=TRUE)

## format the REVIGO result (I have more customized functions downstream, so this
## is probably optional
system(paste("sed -n '/^revigo\\.data.*/,/^stuff.*/p'",
                 fname_out_revigo2,"| egrep '^rev|^c' >", fname_out2))

## load the REVIGO data into your current environment
source(fname_out4)

Answer 2

[Pedro]

Recently I tried with rrvgo package from bioconductor, which is heavily influcenced by REVIGO. And easy to use!