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Subset of genes #119

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gjhuizing opened this issue Sep 2, 2022 · 2 comments
Closed

Subset of genes #119

gjhuizing opened this issue Sep 2, 2022 · 2 comments

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@gjhuizing
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Hello,

Let's say my .rnk file contains 2,500 genes and my .gmt file contains way more. Does fgsea take that into account by subsetting the gene sets to the input genes? Or do I need to manually subset the gene sets?

Thank you,

Geert
@assaron
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assaron commented Sep 2, 2022

fgsea filters out all of the genes, not present in the ranking. You don't have to do it manually.

@gjhuizing
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Great, thank you for the quick reply!

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@assaron @gjhuizing