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lianos / multiGSEA

NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept here for posterity.
https://lianos.github.io/multiGSEA/
MIT License
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Add support for ANOVA-like analyses in multiGSEA() #11

Open lianos opened 6 years ago

lianos commented 6 years ago

Currently we only support testing a specific contrast (either via a coefficient or a contrast vector), but we often do differential expression analysis where we want to test mean shifts in several groups of samples, which we would like to support here.

For instance, if we had a 3-group experiment, ie. a group factor had "control", "treatment01", and "treatment02" levels, we might do a limma analysis like so:

des <- model.matrix(~ group)
fit <- eBayes(lmFit(y, des))
res <- topTable(fit, coef = 2:3, ...)

We want to support that in a GSEA-like manner.

dktanwar commented 5 years ago

Hi @lianos

Is there any update on this?

lianos commented 5 years ago

Yes, there is some basic support for ANVOA analyses followed up with enrichment testing.

I'm only supporting GSEA testing using the "enrichtest" method, which is a wrapper to limma::kegga (which, itself is like goseq).

You can see an example of how that works in this unit test.

I just added that test along with some bugfixes to support that in the latest @develop branch, so you will have to devtools::install_github("lianos/multiGSEA@develop") to get it to work.

Alternatively, you can run the ANOVA (or whatever) test outside of the whole multiGSEA pipeline, and run your enrichment testing using the enrichtest method directly. The examples in ?enrichtest should be enough to get you going.

Let me know if you have any issues.