Question: Rank-based GO enrichment packages for R?
0
gravatar for Dave
3.6 years ago by
Dave70
Japan
Dave70 wrote:

As stated in the title: I am looking for a rank-based (or possibly score-based, but I am not sure any such methods exist) tool for GO enrichment that can be used from R.

All the packages I have found so far (e.g. TopGO) only offer enrichment based on a selected set of genes (possibly obtained through testing). Tools such as GOrilla do it, but only as web-tools. This paper even gives a pretty long list (class II of table 2), but none appear to have an R interface.

Does anyone have experience getting rank-based GO enrichment scores in R?

go R • 1.8k views
ADD COMMENTlink modified 3.6 years ago by Ido Tamir5.0k • written 3.6 years ago by Dave70
0
gravatar for Ido Tamir
3.6 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

https://www.bioconductor.org/packages/release/bioc/html/GSEABase.html

https://www.bioconductor.org/packages/release/BiocViews.html#___GeneSetEnrichment

 

 

 

ADD COMMENTlink written 3.6 years ago by Ido Tamir5.0k

Thanks for trying to answer, but I am afraid you did not really understand the question:

As I wrote, I am aware of the many R packages to do GO enrichment. The problem is that all the ones I have found so far (and indeed, the one you linked) are for gene set enrichment. They require you to specify a set of interest, to compare with the full set.

I am looking for a package that implements one of the existing method to work on ranked list, where no set is specified.

ADD REPLYlink written 3.6 years ago by Dave70

From your own link, where you wanted class 2 and "none appear to have an R interface"

"Class II: gene set enrichment analysis (GSEA)" GSEABase is what you wanted in the question.

 

ADD REPLYlink written 3.6 years ago by Ido Tamir5.0k
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