Convert the output of Enrichr

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

shake_enrichrResult(enrichr_output_file, enrichr_output = NULL)

Arguments

enrichr_output_file

The location of the text file output, as exported from Enrichr

enrichr_output

A data.frame with the output of enrichr, related to a specific set of genesets. Usually it is one of the members of the list returned by the initial call to enrichr.

Value

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

See also

Other shakers: shake_davidResult(), shake_enrichResult(), shake_fgseaResult(), shake_gprofilerResult(), shake_gsenrichResult(), shake_topGOtableResult()

Examples

# library("enrichR")
# dbs <- c("GO_Molecular_Function_2018",
#          "GO_Cellular_Component_2018",
#          "GO_Biological_Process_2018",
#          "KEGG_2019_Human",
#          "Reactome_2016",
#          "WikiPathways_2019_Human")
# degenes <- (mosdef::deresult_to_df(res_macrophage_IFNg_vs_naive, FDR = 0.01)$SYMBOL)
# if called directly within R...
# enrichr_output_macrophage <- enrichr(degenes, dbs)
# or alternatively, if downloaded from the website in tabular format
enrichr_output_file <- system.file("extdata",
  "enrichr_tblexport_IFNg_vs_naive.txt",
  package = "GeneTonic"
)
res_from_enrichr <- shake_enrichrResult(enrichr_output_file = enrichr_output_file)
#> Found 2734 gene sets in the file output from Enrichr of which 514 are significant (p-value <= 0.05).
#> Converting for usage in GeneTonic...
# res_from_enrichr2 <- shake_enrichrResult(
#   enrichr_output = enrichr_output_macrophage[["GO_Biological_Process_2018"]])