Is there a package for ORA where I can supply my own gmt files?

Question

[Gabriel]

I am looking to do standardized Gene Ontology analysis based on a cutoff and Overrepresentation Analysis(ORA, not GSEA).

For this, I've been using gprofiler, etc.

But I need to do this in a standardized way where I can supply my own versioned .gmt files. In topGO, you have to use "their" GO files, and I don't like its over complicated object oriented design. Clusterprofiler was too "high level" for me and not really suitable for a professional study.

I'm looking for a simple package, like GAGE, except for ORA, where I supply -my gmt files -my DEGs -my background genes -pvalue cutoff -Method and other more specific parameters.

Is there a good package in bioconductor where I can do this?

[igor]

I am not sure you need a package. Just use fisher.test().

Answer 1

[Florian]

Hi there,

Maybe I am too late but anyway you can use enricher() clusterProfiler function with your own gmt file.

You could find an example in clusterProfiler vignette with an wikiPathways gmt file: https://yulab-smu.github.io/clusterProfiler-book/chapter3.html#input-data