shake_enrichrResult {GeneTonic} | R Documentation |
Convert the output of Enrichr for straightforward use in GeneTonic()
shake_enrichrResult(enrichr_output_file, enrichr_output = NULL)
enrichr_output_file |
The location of the text file output, as exported from Enrichr |
enrichr_output |
A data.frame with the output of |
A data.frame
compatible for use in GeneTonic()
as res_enrich
Other shakers:
shake_davidResult()
,
shake_enrichResult()
,
shake_fgseaResult()
,
shake_gprofilerResult()
,
shake_gsenrichResult()
,
shake_topGOtableResult()
# 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 <- (deseqresult2df(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) # res_from_enrichr2 <- shake_enrichrResult( # enrichr_output = enrichr_output_macrophage[["GO_Biological_Process_2018"]])