printEnrich: printEnrich

In enrichR: Provides an R Interface to 'Enrichr'

printEnrich

Description

Print Enrichr results

Usage

printEnrich(
  data,
  prefix = "enrichr",
  showTerms = NULL,
  columns = c(1:9),
  outFile = c("txt", "excel")
)

Arguments

data	(Required). Output list object from the "enrichr" function.
prefix	(Optional). Prefix of output file. Default is "enrichr".
showTerms	(Optional). Number of terms to show. Default is NULL to print all terms.
columns	(Optional). Columns from each entry of data. Default is c(1:9) to print all columns. * Results without background: 1-"Term", 2-"Overlap", 3-"P.value", 4-"Adjusted.P.value", 5-"Old.P.value", 6-"Old.Adjusted.P.value", 7-"Odds.Ratio", 8-"Combined.Score", 9-"Combined.Score". * In results with background, the second column is "Rank" if terms are not identical with those annotated in the Enrichr GMT files
outFile	(Optional). Output file format, choose from "txt" and "excel". Default is "txt".

Details

Print Enrichr results from the selected gene-set libraries to individual text files or a Excel spreadsheet.

Author(s)

Wajid Jawaid [e-mail]

I-Hsuan Lin [e-mail]

Examples

# data(input) # Load example input genes
# if (getOption("enrichR.live")) {
#   enrichRLive <- TRUE
#   dbs <- listEnrichrDbs()
#   if(is.null(dbs)) enrichRLive <- FALSE
#   dbs <- c("GO_Molecular_Function_2023", "GO_Cellular_Component_2023",
#            "GO_Biological_Process_2023")
#   enriched <- enrichr(input, dbs)
#   print(head(enriched[[1]]))
#   # if (enrichRLive) printEnrich(enriched, outFile = "excel")
# }

enrichR documentation built on April 4, 2025, 1:07 a.m.