shake_enrichrResult: Convert the output of Enrichr

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Convert the output of Enrichr

Description

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

Usage

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)
# res_from_enrichr2 <- shake_enrichrResult(
#   enrichr_output = enrichr_output_macrophage[["GO_Biological_Process_2018"]])

federicomarini/GeneTonic documentation built on Dec. 21, 2024, 10:05 p.m.