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bioFAM / MOFA

Multi-Omics Factor Analysis
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Feature request: FSEA direction of pathway/factor association #28

Closed whitleyo closed 5 years ago

whitleyo commented 5 years ago

Hi,

I've looked through the man pages and vignettes for the package, and it doesn't appear as if there's any functionality to determine the direction of association of a pathway with a factor. With runEnrichmentAnalysis, correct me if I'm wrong, but you get the result of a two sided test (p-value and adjusted p-value). For a biologist interested in characterizing what the sources of variation are in their data, the direction of association of pathways matter (e.g. how does location in the space of 2 factors determine how stem-like my samples are?). I think it might be a good idea to include the test statistic (e.g. mean difference statistic) in the output.

Thanks

rargelaguet commented 5 years ago

Good point, we will include a more comprehensive output in the next couple of days. For now, you could just color the factors by the expression of the individual genes from the significant pathways:

plotFactorScatter(MOFAobject, factors = 1:2, color_by = "GENE_NAME")

where GENE_NAME has to be a feature that is part of the training data.

rargelaguet commented 5 years ago

Now we include the test statistics in the runEnrichment output and we provide a new function to inspect which genes are driving the signal for each pathway. See plotEnrichmentDetailed.