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ctlab / fgsea

Fast Gene Set Enrichment Analysis
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fgsea for many rank vectors #62

Closed ivokwee closed 4 years ago

ivokwee commented 4 years ago

Hi.

I want to compute fgsea for many rank vectors (hundreds, thousands...) with the same genesets. Currently doing it in a loop or actually wrapped mclapply but it would be nice to let fgsea accept a matrix instead of vector for the stats to avoid any overhead. Would this be faster and feasible?

Ivo

assaron commented 4 years ago

Hi,

We thought of this feature but there is no obvious way to make it work faster compared to a simple *lapply.