Convert the output of fgsea for straightforward use in GeneTonic()

shake_fgseaResult(fgsea_output)

Arguments

fgsea_output

A data.frame with the output of fgsea() in fgsea.

Value

A data.frame compatible for use in GeneTonic() as res_enrich

See also

Examples

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'
#> 
#> 
#> 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