• Software
• EnrichmentMap
• DAVIDgs_R

Convert DAVID gene-sets to GMT format

Instructions

• install R from
  http://cran.r-project.org/

• before running the script, make sure you have changed the working directory to the file location

  • use the GUI menu (e.g., Mac OS: Misc/Change Working Directory)

  • or setwd ("...") where '...' is the path

  • check using list.files () that the file you want to convert is present

• copy-and-paste the following script into the R console

• the output file will be: DAVID.GMT

R Script

file.name <- "..."

gs.df <- read.table (
                        file = file.name,
                        sep  = "\t", header = F, 
                        stringsAsFactors = F,
                        col.names = c ("Eg.ID", "Gs.ID")
                        )

gs.ls <- unstack (gs.df, form = Eg.ID ~ Gs.ID)

cat (
        paste (
                names (gs.ls), names (gs.ls), 
                sapply (gs.ls, paste, collapse = "\t"),
                sep = "\t"
                ), 
        sep = "\n",     
        file = "DAVID.GMT"
        )