R/Run.GSEA.1.0.R

In kmezhoud/canceR: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

#' The  main function to run GSEA-R from Broad Institute
#' @usage
#' Run.GSEA()
#' 
#' @return A vector with sampling size
#' @export
#'
#' @examples
#' readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep=""))
#' \dontrun{
#' Run.GSEA()
#' }
Run.GSEA <- function(){
#   if (!require("GSEABase")) {
#     if (!requireNamespace("BiocManager", quietly=TRUE))
#    install.packages("BioManager")
#    BiocManager::install("GSEABase")
#     library("GSEABase")
#   }
  #source("dialogSelectFiles_GSEA.R")
  
# GSEA 1.0 -- Gene Set Enrichment Analysis / Broad Institute 
#source("dialogSelectFiles_GSEA.R")

#workspace <- getwd()

dialogSelectFiles_GSEA()

##stop the Run when cancelling dialogSelectFiles()
#if(!exists("fname.GSEA")){
#  stop("The GSEA.1.0.R file is not found.")
#}

GSEA.program.location <- paste(path.package("canceR"),"/extdata/GSEA.1.0.R", sep="")
#GSEA.program.location <- fname.GSEA   #  R source program (change pathname to the rigth location in local machine)
source(GSEA.program.location, verbose=TRUE, max.deparse.length=9999)

ENV$prefix <- basename(ENV$fname.Output)

GSEA(                                                                    # Input/Output Files :-------------------------------------------
 input.ds  = ENV$fname.GCT,           # Input gene expression Affy dataset file in RES or GCT format
 input.cls = ENV$fname.CLS,           # Input class vector (phenotype) file in CLS format
 gs.db     = ENV$fname.GMT,         # Gene set database in GMT format
 output.directory      = ENV$fname.Output,        # Directory where to store output and results (default: "")
##  Program parameters :-------------------------------------------------------------------------------------------------------------------------
 doc.string            = ENV$prefix,          # Documentation string used as a prefix to name result files (default: "GSEA.analysis")
 non.interactive.run   = FALSE,               # Run in interactive (i.e. R GUI) or batch (R command line) mode (default: F)
 reshuffling.type      = "sample.labels", # Type of permutation reshuffling: "sample.labels" or "gene.labels" (default: "sample.labels" 
 nperm                 = 1000,            # Number of random permutations (default: 1000)
 weighted.score.type   =  1,              # Enrichment correlation-based weighting: 0=no weight (KS), 1= weigthed, 2 = over-weigthed (default: 1)
 nom.p.val.threshold   = -1,              # Significance threshold for nominal p-vals for gene sets (default: -1, no thres)
 fwer.p.val.threshold  = -1,              # Significance threshold for FWER p-vals for gene sets (default: -1, no thres)
 fdr.q.val.threshold   = 0.25,            # Significance threshold for FDR q-vals for gene sets (default: 0.25)
 topgs                 = 20,              # Besides those passing test, number of top scoring gene sets used for detailed reports (default: 10)
 adjust.FDR.q.val      = FALSE,               # Adjust the FDR q-vals (default: F)
 gs.size.threshold.min = 15,              # Minimum size (in genes) for database gene sets to be considered (default: 25)
 gs.size.threshold.max = 500,             # Maximum size (in genes) for database gene sets to be considered (default: 500)
 reverse.sign          = FALSE,               # Reverse direction of gene list (pos. enrichment becomes negative, etc.) (default: F)
 preproc.type          = 0,               # Preproc.normalization: 0=none, 1=col(z-score)., 2=col(rank) and row(z-score)., 3=col(rank). (def: 0)
 random.seed           = 3338,            # Random number generator seed. (default: 123456)
 perm.type             = 0,               # For experts only. Permutation type: 0 = unbalanced, 1 = balanced (default: 0)
 fraction              = 1.0,             # For experts only. Subsampling fraction. Set to 1.0 (no resampling) (default: 1.0)
 replace               = FALSE,               # For experts only, Resampling mode (replacement or not replacement) (default: F)
 save.intermediate.results = FALSE,           # For experts only, save intermediate results (e.g. matrix of random perm. scores) (default: F)
 OLD.GSEA              = FALSE,               # Use original (old) version of GSEA (default: F)
 use.fast.enrichment.routine = TRUE          # Use faster routine to compute enrichment for random permutations (default: T)
)
#-----------------------------------------------------------------------------------------------------------------------------------------------

# Overlap and leading gene subset assignment analysis of the GSEA results

GSEA.Analyze.Sets(
  directory           = ENV$fname.Output,        # Directory where to store output and results (default: "")
   topgs = 20,                              # number of top scoring gene sets used for analysis
   non.interactive.run = FALSE,
   height = 16,
   width = 16
)

}