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ctlab / phantasus

Visual exploratory analysis of gene expression data
https://alserglab.wustl.edu/phantasus/
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How to use fgsea? #115

Closed shashj closed 5 years ago

shashj commented 5 years ago

Hi, I am very much interested to use fgsea in phantasus. I understand that we need to provide fgsea meta files, how do we provide them? A little help and direction will be of huge help.

Thanks

vlakam commented 5 years ago

Hi.

You need to generate list with columns ("geneID", "pathName", "geneSymbol") and place it under cacheDir/fgsea in .rds format

---edit

By the way, geneSymbol column is actually optional. Its just to let user know which genes in the pathway on click. FGSEA works on geneIDs. dbExample.zip Here is example with one pathway w\o Gene Symbols

shashj commented 5 years ago

@vlakam Thank you so much it works. Just a question, if I click on some pathway to check the genes it throws some error

Screen Shot 2019-04-06 at 12 01 44 AM

shashj commented 5 years ago

@vlakam Don't worry I figured it out, we have to give gene symbols as well