what does gseaparam argument in fgsea() means?
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kavator ▴ 20
@kavator-22955
Last seen 15 months ago

Hi everyone I dont really have problems running fgsea itself but im trying to understand what gseaparam argument in fgsea() means. The vignette says it's a GSEA weight parameter. but weightage of what? each fgsea term? and to what exactly

hope to hear some clarifications; tried googling it's still not clear to me.

fgsea • 447 views
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assaron ▴ 200
@assaron
Last seen 5 weeks ago
St Petersburg

This is the power, to which all input gene-level stats are raised to. If gseaParam is zero, then all gene-level stats effectively become ones and GSEA test becomes Kolmogorov-Smirnov test. The default value of gseaParam is one, meaning that gene-level stats are used as is.

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Thank you; how do we know the implications of altering the gseaParam and the best practices of it? Feel free to link me to other resources/papers. thanks

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