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bioFAM / MOFA

Multi-Omics Factor Analysis
GNU Lesser General Public License v3.0
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Enrichment analysis with HUGO symbols #42

Closed merlevede closed 5 years ago

merlevede commented 5 years ago

Hello,

I am trying your tools on few datasets. For all of them, I have HUGO symbols for feature names. So when trying to perform feature set enrichment analysis, I get an error:

gsea <- runEnrichmentAnalysis( MOFAobject, view = "mRNA", feature.sets = reactomeGS, alpha = 0.01 ) Error in runEnrichmentAnalysis(MOFAobject, view = "mRNA", feature.sets = reactomeGS, : Feautre names in feature.sets do not match feature names in model.

Is there a way to use HUGO symbols instead of ensembl annotations for feature.sets for enrichment analysis (using Reactome or other databases)?

Thank you in advance, Jane

rargelaguet commented 5 years ago

Hi Jane,

You have two options: (1) use the gene set annotations that I prepared, but you will have to manually convert the ensemble IDs to HUGO IDs (i.e. just change the column names of reactomeGS). (2) create your own gene set annotations with HUGO IDs and provide them as input to runEnrichmentAnalysis. The format is a binary matrix with pathways in the rows and features in the columns.

merlevede commented 5 years ago

Thank you for your answer. I will then convert the ID given in feature.sets. It might be user friendly to give the choice between annotations if there is a next release of MOFA.