Convert the output of fgsea for straightforward use in GeneTonic()
shake_fgseaResult(fgsea_output)A data.frame with the output of fgsea() in fgsea.
A data.frame compatible for use in GeneTonic() as res_enrich
Other shakers:
shake_davidResult(),
shake_enrichResult(),
shake_enrichrResult(),
shake_gprofilerResult(),
shake_gsenrichResult(),
shake_topGOtableResult()
data(fgseaRes, package = "GeneTonic")
res_from_fgsea <- shake_fgseaResult(fgseaRes)
#> Found 7341 gene sets in the file output from Enrichr of which 102 are significant (p-value <= 0.05).
#> Converting for usage in GeneTonic...
#> Using the content of the 'leadingEdge' column to generate the 'gs_genes' for GeneTonic... If you have that information available directly, please adjust the content accordingly.
#>
#> Using the set of the leadingEdge size to compute the 'gs_de_count'
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#> fgsea is commonly returning no identifier for the gene sets used. Please consider editing the 'gs_id' field manually according to the gene set you provided