shake_enrichrResult: Convert the output of Enrichr

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

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_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 <- (deseqresult2df(res_macrophage_IFNg_vs_naive, FDR = 0.01)$SYMBOL)
# if called directly withín 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"]])

GeneTonic documentation built on Nov. 8, 2020, 5:27 p.m.