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Minimum logFC value not honored from shiny input of ffsea ORA config UI #42

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lianos opened this issue Oct 6, 2020 · 1 comment
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lianos commented Oct 6, 2020

When a user alters the minimum logFC required for the overrepresentation analysis in ffsea via shiny, it's not being passed down to the ffsea call.

Files to look at:

  1. The shiny UI is whipped up in ffsea-shiny-runOptions.R ~ line 166 (renderFfseaRunOptsUI.FacileTtestAnalysisResult())
  2. The shiny invocation of ffsea in fsea-shiny.R ~ line 176
@lianos lianos added the bug Something isn't working label Oct 6, 2020
@lianos lianos self-assigned this Oct 6, 2020
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lianos commented Oct 6, 2020

It looks like the ffsea.FacileTtestAnalysisResult function is setting the significant column in the input data.frame correctly based on those parameters, but we're dropping a beat somewhere within multiGSEA with the significant column already set and perhaps the feature.max.padj and feature.min.logFC parameters it maybe expected to use.

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