R/gsea.R

In hxin/gsea: What the package does (short line)

# The Broad Institute
# SOFTWARE COPYRIGHT NOTICE AGREEMENT
# This software and its documentation are copyright 2003 by the
# Broad Institute/Massachusetts Institute of Technology.
# All rights are reserved.
#
# This software is supplied without any warranty or guaranteed support
# whatsoever. Neither the Broad Institute nor MIT can be responsible for
# its use, misuse, or functionality.


# G S E A -- Gene Set Enrichment Analysis

# Auxiliary functions and definitions 

GSEA.GeneRanking <- function(A, class.labels, gene.labels, nperm, permutation.type = 0, sigma.correction = "GeneCluster", fraction=1.0, replace=F, reverse.sign= F) { 
  
  # This function ranks the genes according to the signal to noise ratio for the actual phenotype and also random permutations and bootstrap  
  # subsamples of both the observed and random phenotypes. It uses matrix operations to implement the signal to noise calculation 
  # in stages and achieves fast execution speed. It supports two types of permutations: random (unbalanced) and balanced. 
  # It also supports subsampling and bootstrap by using masking and multiple-count variables.  When "fraction" is set to 1 (default)
  # the there is no subsampling or boostrapping and the matrix of observed signal to noise ratios will have the same value for 
  # all permutations. This is wasteful but allows to support all the multiple options with the same code. Notice that the second 
  # matrix for the null distribution will still have the values for the random permutations 
  # (null distribution). This mode (fraction = 1.0) is the defaults, the recommended one and the one used in the examples.
  # It is also the one that has be tested more thoroughly. The resampling and boostrapping options are intersting to obtain 
  # smooth estimates of the observed distribution but its is left for the expert user who may want to perform some sanity 
  # checks before trusting the code.
  #
  # Inputs:
  #   A: Matrix of gene expression values (rows are genes, columns are samples) 
  #   class.labels: Phenotype of class disticntion of interest. A vector of binary labels having first the 1's and then the 0's 
  #   gene.labels: gene labels. Vector of probe ids or accession numbers for the rows of the expression matrix 
  #   nperm: Number of random permutations/bootstraps to perform 
  #   permutation.type: Permutation type: 0 = unbalanced, 1 = balanced. For experts only (default: 0) 
  #   sigma.correction: Correction to the signal to noise ratio (Default = GeneCluster, a choice to support the way it was handled in a previous package) 
  #   fraction: Subsampling fraction. Set to 1.0 (no resampling). For experts only (default: 1.0) 
  #   replace: Resampling mode (replacement or not replacement). For experts only (default: F) 
  #   reverse.sign: Reverse direction of gene list (default = F)
  #
  # Outputs:
  #   s2n.matrix: Matrix with random permuted or bootstraps signal to noise ratios (rows are genes, columns are permutations or bootstrap subsamplings
  #   obs.s2n.matrix: Matrix with observed signal to noise ratios (rows are genes, columns are boostraps subsamplings. If fraction is set to 1.0 then all the columns have the same values
  #   order.matrix: Matrix with the orderings that will sort the columns of the obs.s2n.matrix in decreasing s2n order
  #   obs.order.matrix: Matrix with the orderings that will sort the columns of the s2n.matrix in decreasing s2n order
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  A <- A + 0.00000001
  
  N <- length(A[,1])
  Ns <- length(A[1,])
  
  subset.mask <- matrix(0, nrow=Ns, ncol=nperm)
  reshuffled.class.labels1 <- matrix(0, nrow=Ns, ncol=nperm)
  reshuffled.class.labels2 <- matrix(0, nrow=Ns, ncol=nperm)
  class.labels1 <- matrix(0, nrow=Ns, ncol=nperm)
  class.labels2 <- matrix(0, nrow=Ns, ncol=nperm)
  
  order.matrix <- matrix(0, nrow = N, ncol = nperm)
  obs.order.matrix <- matrix(0, nrow = N, ncol = nperm)
  s2n.matrix <- matrix(0, nrow = N, ncol = nperm)
  obs.s2n.matrix <- matrix(0, nrow = N, ncol = nperm)
  
  obs.gene.labels <- vector(length = N, mode="character")
  obs.gene.descs <- vector(length = N, mode="character")
  obs.gene.symbols <- vector(length = N, mode="character")
  
  M1 <- matrix(0, nrow = N, ncol = nperm)
  M2 <- matrix(0, nrow = N, ncol = nperm)
  S1 <- matrix(0, nrow = N, ncol = nperm)
  S2 <- matrix(0, nrow = N, ncol = nperm)
  
  gc()
  
  C <- split(class.labels, class.labels)
  class1.size <- length(C[[1]])
  class2.size <- length(C[[2]])
  class1.index <- seq(1, class1.size, 1)
  class2.index <- seq(class1.size + 1, class1.size + class2.size, 1)
  
  for (r in 1:nperm) {
    class1.subset <- sample(class1.index, size = ceiling(class1.size*fraction), replace = replace)
    class2.subset <- sample(class2.index, size = ceiling(class2.size*fraction), replace = replace)
    class1.subset.size <- length(class1.subset)
    class2.subset.size <- length(class2.subset)
    subset.class1 <- rep(0, class1.size)
    for (i in 1:class1.size) {
      if (is.element(class1.index[i], class1.subset)) {
        subset.class1[i] <- 1
      }
    }
    subset.class2 <- rep(0, class2.size)
    for (i in 1:class2.size) {
      if (is.element(class2.index[i], class2.subset)) {
        subset.class2[i] <- 1
      }
    }
    subset.mask[, r] <- as.numeric(c(subset.class1, subset.class2))
    fraction.class1 <- class1.size/Ns
    fraction.class2 <- class2.size/Ns
    
    if (permutation.type == 0) { # random (unbalanced) permutation
      full.subset <- c(class1.subset, class2.subset)
      label1.subset <- sample(full.subset, size = Ns * fraction.class1)
      reshuffled.class.labels1[, r] <- rep(0, Ns)
      reshuffled.class.labels2[, r] <- rep(0, Ns)
      class.labels1[, r] <- rep(0, Ns)
      class.labels2[, r] <- rep(0, Ns)
      for (i in 1:Ns) {
        m1 <- sum(!is.na(match(label1.subset, i)))
        m2 <- sum(!is.na(match(full.subset, i)))
        reshuffled.class.labels1[i, r] <- m1
        reshuffled.class.labels2[i, r] <- m2 - m1
        if (i <= class1.size) {
          class.labels1[i, r] <- m2
          class.labels2[i, r] <- 0
        } else {
          class.labels1[i, r] <- 0
          class.labels2[i, r] <- m2
        }
      }
      
    } else if (permutation.type == 1) { # proportional (balanced) permutation
      
      class1.label1.subset <- sample(class1.subset, size = ceiling(class1.subset.size*fraction.class1))
      class2.label1.subset <- sample(class2.subset, size = floor(class2.subset.size*fraction.class1))
      reshuffled.class.labels1[, r] <- rep(0, Ns)
      reshuffled.class.labels2[, r] <- rep(0, Ns)
      class.labels1[, r] <- rep(0, Ns)
      class.labels2[, r] <- rep(0, Ns)
      for (i in 1:Ns) {
        if (i <= class1.size) {
          m1 <- sum(!is.na(match(class1.label1.subset, i)))
          m2 <- sum(!is.na(match(class1.subset, i)))
          reshuffled.class.labels1[i, r] <- m1
          reshuffled.class.labels2[i, r] <- m2 - m1
          class.labels1[i, r] <- m2
          class.labels2[i, r] <- 0
        } else {
          m1 <- sum(!is.na(match(class2.label1.subset, i)))
          m2 <- sum(!is.na(match(class2.subset, i)))
          reshuffled.class.labels1[i, r] <- m1
          reshuffled.class.labels2[i, r] <- m2 - m1
          class.labels1[i, r] <- 0
          class.labels2[i, r] <- m2
        }
      }
    }
  }
  
  # compute S2N for the random permutation matrix
  ##from each, randomly take X samples from the two class lables and get the mean as the null value of that gene's expression
  P <- reshuffled.class.labels1 * subset.mask
  n1 <- sum(P[,1])         
  M1 <- A %*% P
  M1 <- M1/n1      
  gc()
  A2 <- A*A        
  S1 <- A2 %*% P   
  S1 <- S1/n1 - M1*M1    
  S1 <- sqrt(abs((n1/(n1-1)) * S1))   
  gc()
  P <- reshuffled.class.labels2 * subset.mask
  n2 <- sum(P[,1])           
  M2 <- A %*% P           
  M2 <- M2/n2          
  gc()
  A2 <- A*A           
  S2 <- A2 %*% P      
  S2 <- S2/n2 - M2*M2 
  S2 <- sqrt(abs((n2/(n2-1)) * S2))
  rm(P)
  rm(A2)
  gc()
  
  if (sigma.correction == "GeneCluster") {  # small sigma "fix" as used in GeneCluster
    S2 <- ifelse(0.2*abs(M2) < S2, S2, 0.2*abs(M2))
    S2 <- ifelse(S2 == 0, 0.2, S2)
    S1 <- ifelse(0.2*abs(M1) < S1, S1, 0.2*abs(M1))
    S1 <- ifelse(S1 == 0, 0.2, S1)
    gc()
  }
  
  M1 <- M1 - M2
  rm(M2)
  gc()
  S1 <- S1 + S2
  rm(S2)
  gc()
  
  s2n.matrix <- M1/S1
  
  if (reverse.sign == T) {
    s2n.matrix <- - s2n.matrix
  }
  gc()
  
  for (r in 1:nperm) {
    order.matrix[, r] <- order(s2n.matrix[, r], decreasing=T)            
  }
  
  # compute S2N for the "observed" permutation matrix
  
  P <- class.labels1 * subset.mask
  n1 <- sum(P[,1])         
  M1 <- A %*% P
  M1 <- M1/n1      
  gc()
  A2 <- A*A        
  S1 <- A2 %*% P   
  S1 <- S1/n1 - M1*M1    
  S1 <- sqrt(abs((n1/(n1-1)) * S1))   
  gc()
  P <- class.labels2 * subset.mask
  n2 <- sum(P[,1])           
  M2 <- A %*% P           
  M2 <- M2/n2          
  gc()
  A2 <- A*A           
  S2 <- A2 %*% P      
  S2 <- S2/n2 - M2*M2 
  S2 <- sqrt(abs((n2/(n2-1)) * S2))
  rm(P)
  rm(A2)
  gc()
  
  if (sigma.correction == "GeneCluster") {  # small sigma "fix" as used in GeneCluster
    S2 <- ifelse(0.2*abs(M2) < S2, S2, 0.2*abs(M2))
    S2 <- ifelse(S2 == 0, 0.2, S2)
    S1 <- ifelse(0.2*abs(M1) < S1, S1, 0.2*abs(M1))
    S1 <- ifelse(S1 == 0, 0.2, S1)
    gc()
  } 
  
  M1 <- M1 - M2
  rm(M2)
  gc()
  S1 <- S1 + S2
  rm(S2)
  gc()
  
  obs.s2n.matrix <- M1/S1
  gc()
  
  if (reverse.sign == T) {
    obs.s2n.matrix <- - obs.s2n.matrix
  }
  
  for (r in 1:nperm) {
    obs.order.matrix[,r] <- order(obs.s2n.matrix[,r], decreasing=T)            
  }
  
  return(list(s2n.matrix = s2n.matrix, 
              obs.s2n.matrix = obs.s2n.matrix, 
              order.matrix = order.matrix,
              obs.order.matrix = obs.order.matrix))
}

GSEA.EnrichmentScore <- function(gene.list, gene.set, weighted.score.type = 1, correl.vector = NULL) {  
  #
  # Computes the weighted GSEA score of gene.set in gene.list. 
  # The weighted score type is the exponent of the correlation 
  # weight: 0 (unweighted = Kolmogorov-Smirnov), 1 (weighted), and 2 (over-weighted). When the score type is 1 or 2 it is 
  # necessary to input the correlation vector with the values in the same order as in the gene list.
  #
  # Inputs:
  #   gene.list: The ordered gene list (e.g. integers indicating the original position in the input dataset)  
  #   gene.set: A gene set (e.g. integers indicating the location of those genes in the input dataset) 
  #   weighted.score.type: Type of score: weight: 0 (unweighted = Kolmogorov-Smirnov), 1 (weighted), and 2 (over-weighted)  
  #  correl.vector: A vector with the coorelations (e.g. signal to noise scores) corresponding to the genes in the gene list 
  #
  # Outputs:
  #   ES: Enrichment score (real number between -1 and +1) 
  #   arg.ES: Location in gene.list where the peak running enrichment occurs (peak of the "mountain") 
  #   RES: Numerical vector containing the running enrichment score for all locations in the gene list 
  #   tag.indicator: Binary vector indicating the location of the gene sets (1's) in the gene list 
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  tag.indicator <- sign(match(gene.list, gene.set, nomatch=0))    # notice that the sign is 0 (no tag) or 1 (tag) 
  no.tag.indicator <- 1 - tag.indicator 
  N <- length(gene.list) 
  Nh <- length(gene.set) 
  Nm <-  N - Nh 
  if (weighted.score.type == 0) {
    correl.vector <- rep(1, N)
  }
  alpha <- weighted.score.type
  correl.vector <- abs(correl.vector**alpha)
  sum.correl.tag    <- sum(correl.vector[tag.indicator == 1])
  norm.tag    <- 1.0/sum.correl.tag
  norm.no.tag <- 1.0/Nm
  RES <- cumsum(tag.indicator * correl.vector * norm.tag - no.tag.indicator * norm.no.tag)      
  max.ES <- max(RES)
  min.ES <- min(RES)
  if (max.ES > - min.ES) {
    #      ES <- max.ES
    ES <- signif(max.ES, digits = 5)
    arg.ES <- which.max(RES)
  } else {
    #      ES <- min.ES
    ES <- signif(min.ES, digits=5)
    arg.ES <- which.min(RES)
  }
  return(list(ES = ES, arg.ES = arg.ES, RES = RES, indicator = tag.indicator))    
}


OLD.GSEA.EnrichmentScore <- function(gene.list, gene.set) {  
  #
  # Computes the original GSEA score from Mootha et al 2003 of gene.set in gene.list 
  #
  # Inputs:
  #   gene.list: The ordered gene list (e.g. integers indicating the original position in the input dataset)  
  #   gene.set: A gene set (e.g. integers indicating the location of those genes in the input dataset) 
  #
  # Outputs:
  #   ES: Enrichment score (real number between -1 and +1) 
  #   arg.ES: Location in gene.list where the peak running enrichment occurs (peak of the "mountain") 
  #   RES: Numerical vector containing the running enrichment score for all locations in the gene list 
  #   tag.indicator: Binary vector indicating the location of the gene sets (1's) in the gene list 
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  tag.indicator <- sign(match(gene.list, gene.set, nomatch=0))    # notice that the sign is 0 (no tag) or 1 (tag) 
  no.tag.indicator <- 1 - tag.indicator 
  N <- length(gene.list) 
  Nh <- length(gene.set) 
  Nm <-  N - Nh 
  
  norm.tag    <- sqrt((N - Nh)/Nh)
  norm.no.tag <- sqrt(Nh/(N - Nh))
  
  RES <- cumsum(tag.indicator * norm.tag - no.tag.indicator * norm.no.tag)      
  max.ES <- max(RES)
  min.ES <- min(RES)
  if (max.ES > - min.ES) {
    ES <- signif(max.ES, digits=5)
    arg.ES <- which.max(RES)
  } else {
    ES <- signif(min.ES, digits=5)
    arg.ES <- which.min(RES)
  }
  return(list(ES = ES, arg.ES = arg.ES, RES = RES, indicator = tag.indicator))    
}

GSEA.EnrichmentScore2 <- function(gene.list, gene.set, weighted.score.type = 1, correl.vector = NULL) {  
  #
  # Computes the weighted GSEA score of gene.set in gene.list. It is the same calculation as in 
  # GSEA.EnrichmentScore but faster (x8) without producing the RES, arg.RES and tag.indicator outputs.
  # This call is intended to be used to asses the enrichment of random permutations rather than the 
  # observed one.
  # The weighted score type is the exponent of the correlation 
  # weight: 0 (unweighted = Kolmogorov-Smirnov), 1 (weighted), and 2 (over-weighted). When the score type is 1 or 2 it is 
  # necessary to input the correlation vector with the values in the same order as in the gene list.
  #
  # Inputs:
  #   gene.list: The ordered gene list (e.g. integers indicating the original position in the input dataset)  
  #   gene.set: A gene set (e.g. integers indicating the location of those genes in the input dataset) 
  #   weighted.score.type: Type of score: weight: 0 (unweighted = Kolmogorov-Smirnov), 1 (weighted), and 2 (over-weighted)  
  #  correl.vector: A vector with the coorelations (e.g. signal to noise scores) corresponding to the genes in the gene list 
  #
  # Outputs:
  #   ES: Enrichment score (real number between -1 and +1) 
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  N <- length(gene.list) 
  Nh <- length(gene.set) 
  Nm <-  N - Nh 
  
  loc.vector <- vector(length=N, mode="numeric")
  peak.res.vector <- vector(length=Nh, mode="numeric")
  valley.res.vector <- vector(length=Nh, mode="numeric")
  tag.correl.vector <- vector(length=Nh, mode="numeric")
  tag.diff.vector <- vector(length=Nh, mode="numeric")
  tag.loc.vector <- vector(length=Nh, mode="numeric")
  
  loc.vector[gene.list] <- seq(1, N)
  tag.loc.vector <- loc.vector[gene.set]
  
  tag.loc.vector <- sort(tag.loc.vector, decreasing = F)
  
  if (weighted.score.type == 0) {
    tag.correl.vector <- rep(1, Nh)
  } else if (weighted.score.type == 1) {
    tag.correl.vector <- correl.vector[tag.loc.vector]
    tag.correl.vector <- abs(tag.correl.vector)
  } else if (weighted.score.type == 2) {
    tag.correl.vector <- correl.vector[tag.loc.vector]*correl.vector[tag.loc.vector]
    tag.correl.vector <- abs(tag.correl.vector)
  } else {
    tag.correl.vector <- correl.vector[tag.loc.vector]**weighted.score.type
    tag.correl.vector <- abs(tag.correl.vector)
  }
  
  norm.tag <- 1.0/sum(tag.correl.vector)
  tag.correl.vector <- tag.correl.vector * norm.tag
  norm.no.tag <- 1.0/Nm
  tag.diff.vector[1] <- (tag.loc.vector[1] - 1) 
  tag.diff.vector[2:Nh] <- tag.loc.vector[2:Nh] - tag.loc.vector[1:(Nh - 1)] - 1
  tag.diff.vector <- tag.diff.vector * norm.no.tag
  peak.res.vector <- cumsum(tag.correl.vector - tag.diff.vector)
  valley.res.vector <- peak.res.vector - tag.correl.vector
  max.ES <- max(peak.res.vector)
  min.ES <- min(valley.res.vector)
  ES <- signif(ifelse(max.ES > - min.ES, max.ES, min.ES), digits=5)
  
  return(list(ES = ES))
  
}

GSEA.HeatMapPlot <- function(V, row.names = F, col.labels, col.classes, col.names = F, main = " ", xlab=" ", ylab=" ") {
  #
  # Plots a heatmap "pinkogram" of a gene expression matrix including phenotype vector and gene, sample and phenotype labels
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  n.rows <- length(V[,1])
  n.cols <- length(V[1,])
  row.mean <- apply(V, MARGIN=1, FUN=mean)
  row.sd <- apply(V, MARGIN=1, FUN=sd)
  row.n <- length(V[,1])
  for (i in 1:n.rows) {
    if (row.sd[i] == 0) {
      V[i,] <- 0
    } else {
      V[i,] <- (V[i,] - row.mean[i])/(0.5 * row.sd[i])
    }
    V[i,] <- ifelse(V[i,] < -6, -6, V[i,])
    V[i,] <- ifelse(V[i,] > 6, 6, V[i,])
  }
  
  mycol <- c("#0000FF", "#0000FF", "#4040FF", "#7070FF", "#8888FF", "#A9A9FF", "#D5D5FF", "#EEE5EE", "#FFAADA", "#FF9DB0", "#FF7080", "#FF5A5A", "#FF4040", "#FF0D1D", "#FF0000") # blue-pinkogram colors. The first and last are the colors to indicate the class vector (phenotype). This is the 1998-vintage, pre-gene cluster, original pinkogram color map
  
  mid.range.V <- mean(range(V)) - 0.1
  heatm <- matrix(0, nrow = n.rows + 1, ncol = n.cols)
  heatm[1:n.rows,] <- V[seq(n.rows, 1, -1),]
  heatm[n.rows + 1,] <- ifelse(col.labels == 0, 7, -7)
  image(1:n.cols, 1:(n.rows + 1), t(heatm), col=mycol, axes=FALSE, main=main, xlab= xlab, ylab=ylab)
  
  if (length(row.names) > 1) {
    numC <- nchar(row.names)
    size.row.char <- 35/(n.rows + 5)
    size.col.char <- 25/(n.cols + 5)
    maxl <- floor(n.rows/1.6)
    for (i in 1:n.rows) {
      row.names[i] <- substr(row.names[i], 1, maxl)
    }
    row.names <- c(row.names[seq(n.rows, 1, -1)], "Class")
    axis(2, at=1:(n.rows + 1), labels=row.names, adj= 0.5, tick=FALSE, las = 1, cex.axis=size.row.char, font.axis=2, line=-1)
  }
  
  if (length(col.names) > 1) {
    axis(1, at=1:n.cols, labels=col.names, tick=FALSE, las = 3, cex.axis=size.col.char, font.axis=2, line=-1)
  }
  
  C <- split(col.labels, col.labels)
  class1.size <- length(C[[1]])
  class2.size <- length(C[[2]])
  axis(3, at=c(floor(class1.size/2),class1.size + floor(class2.size/2)), labels=col.classes, tick=FALSE, las = 1, cex.axis=1.25, font.axis=2, line=-1)
  
  return()
}

GSEA.Res2Frame <- function(filename = "NULL") { 
  #
  # Reads a gene expression dataset in RES format and converts it into an R data frame
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  header.cont <- readLines(filename, n = 1)
  temp <- unlist(strsplit(header.cont, "\t"))
  colst <- length(temp)
  header.labels <- temp[seq(3, colst, 2)]
  ds <- read.delim(filename, header=F, row.names = 2, sep="\t", skip=3, blank.lines.skip=T, comment.char="", as.is=T)
  colst <- length(ds[1,])
  cols <- (colst - 1)/2
  rows <- length(ds[,1])
  A <- matrix(nrow=rows - 1, ncol=cols)
  A <- ds[1:rows, seq(2, colst, 2)]
  table1 <- data.frame(A)
  names(table1) <- header.labels
  return(table1)
}

GSEA.Gct2Frame <- function(filename = "NULL") { 
  #
  # Reads a gene expression dataset in GCT format and converts it into an R data frame
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  ds <- read.delim(filename, header=T, sep="\t", skip=2, row.names=1, blank.lines.skip=T, comment.char="", as.is=T)
  ds <- ds[-1]
  return(ds)
}

GSEA.Gct2Frame2 <- function(filename = "NULL") { 
  #
  # Reads a gene expression dataset in GCT format and converts it into an R data frame
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  content <- readLines(filename)
  content <- content[-1]
  content <- content[-1]
  col.names <- noquote(unlist(strsplit(content[1], "\t")))
  col.names <- col.names[c(-1, -2)]
  num.cols <- length(col.names)
  content <- content[-1]
  content <- content[which(content!="")]
  num.lines <- length(content)
  
  
  row.nam <- vector(length=num.lines, mode="character")
  row.des <- vector(length=num.lines, mode="character")
  m <- matrix(0, nrow=num.lines, ncol=num.cols)
  
  for (i in 1:num.lines) {
    line.list <- noquote(unlist(strsplit(content[i], "\t")))
    row.nam[i] <- noquote(line.list[1])
    row.des[i] <- noquote(line.list[2])
    line.list <- line.list[c(-1, -2)]
    for (j in 1:length(line.list)) {
      m[i, j] <- as.numeric(line.list[j])
    }
  }
  ds <- data.frame(m)
  names(ds) <- col.names
  row.names(ds) <- row.nam
  return(ds)
}

GSEA.ReadClsFile <- function(file = "NULL") { 
  #
  # Reads a class vector CLS file and defines phenotype and class labels vectors for the samples in a gene expression file (RES or GCT format)
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  cls.cont <- readLines(file)
  num.lines <- length(cls.cont)
  class.list <- unlist(strsplit(cls.cont[[3]], " "))
  s <- length(class.list)
  t <- table(class.list)
  l <- length(t)
  phen <- vector(length=l, mode="character")
  phen.label <- vector(length=l, mode="numeric")
  class.v <- vector(length=s, mode="numeric")
  for (i in 1:l) {
    phen[i] <- noquote(names(t)[i])
    phen.label[i] <- i - 1
  }
  for (i in 1:s) {
    for (j in 1:l) {
      if (class.list[i] == phen[j]) {
        class.v[i] <- phen.label[j]
      }
    }
  }
  return(list(phen = phen, class.v = class.v))
}

GSEA.Threshold <- function(V, thres, ceil) { 
  #
  # Threshold and ceiling pre-processing for gene expression matrix
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  V[V < thres] <- thres
  V[V > ceil] <- ceil
  return(V)
}

GSEA.VarFilter <- function(V, fold, delta, gene.names = "NULL") { 
  #
  # Variation filter pre-processing for gene expression matrix
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  cols <- length(V[1,])
  rows <- length(V[,1])
  row.max <- apply(V, MARGIN=1, FUN=max)
  row.min <- apply(V, MARGIN=1, FUN=min)
  flag <- array(dim=rows)
  flag <- (row.max /row.min > fold) & (row.max - row.min > delta)
  size <- sum(flag)
  B <- matrix(0, nrow = size, ncol = cols)
  j <- 1
  if (gene.names == "NULL") {
    for (i in 1:rows) {
      if (flag[i]) {
        B[j,] <- V[i,]
        j <- j + 1
      }
    }
    return(B)
  } else {
    new.list <- vector(mode = "character", length = size)
    for (i in 1:rows) {
      if (flag[i]) {
        B[j,] <- V[i,]
        new.list[j] <- gene.names[i]
        j <- j + 1
      }
    }
    return(list(V = B, new.list = new.list))
  }
}

GSEA.NormalizeRows <- function(V) { 
  #
  # Stardardize rows of a gene expression matrix
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  row.mean <- apply(V, MARGIN=1, FUN=mean)
  row.sd <- apply(V, MARGIN=1, FUN=sd)
  row.n <- length(V[,1])
  for (i in 1:row.n) {
    if (row.sd[i] == 0) {
      V[i,] <- 0
    } else {
      V[i,] <- (V[i,] - row.mean[i])/row.sd[i]
    }
  }
  return(V)
}

GSEA.NormalizeCols <- function(V) { 
  #
  # Stardardize columns of a gene expression matrix
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  col.mean <- apply(V, MARGIN=2, FUN=mean)
  col.sd <- apply(V, MARGIN=2, FUN=sd)
  col.n <- length(V[1,])
  for (i in 1:col.n) {
    if (col.sd[i] == 0) {
      V[i,] <- 0
    } else {
      V[,i] <- (V[,i] - col.mean[i])/col.sd[i]
    }
  }
  return(V)
}

# end of auxiliary functions

# ----------------------------------------------------------------------------------------
# Main GSEA Analysis Function that implements the entire methodology

GSEA <- function(
  input.ds, 
  input.cls, 
  gene.ann = "", 
  gs.db, 
  gs.ann = "",
  output.directory = "", 
  doc.string = "GSEA.analysis", 
  non.interactive.run = F, 
  reshuffling.type = "sample.labels", 
  nperm = 1000, 
  weighted.score.type = 1, 
  nom.p.val.threshold = -1, 
  fwer.p.val.threshold = -1, 
  fdr.q.val.threshold = 0.25, 
  topgs = 10,
  adjust.FDR.q.val = F, 
  gs.size.threshold.min = 25, 
  gs.size.threshold.max = 500, 
  reverse.sign = F, 
  preproc.type = 0, 
  random.seed = 123456, 
  perm.type = 0, 
  fraction = 1.0, 
  replace = F,
  save.intermediate.results = F,
  OLD.GSEA = F,
  use.fast.enrichment.routine = T) {
  
  # This is a methodology for the analysis of global molecular profiles called Gene Set Enrichment Analysis (GSEA). It determines 
  # whether an a priori defined set of genes shows statistically significant, concordant differences between two biological 
  # states (e.g. phenotypes). GSEA operates on all genes from an experiment, rank ordered by the signal to noise ratio and 
  # determines whether members of an a priori defined gene set are nonrandomly distributed towards the top or bottom of the 
  # list and thus may correspond to an important biological process. To assess significance the program uses an empirical 
  # permutation procedure to test deviation from random that preserves correlations between genes. 
  #
  # For details see Subramanian et al 2005
  #
  # Inputs:
  #   input.ds: Input gene expression Affymetrix dataset file in RES or GCT format 
  #   input.cls:  Input class vector (phenotype) file in CLS format 
  #   gene.ann.file: Gene microarray annotation file (Affymetrix Netaffyx *.csv format) (default: none) 
  #   gs.file: Gene set database in GMT format 
  #   output.directory: Directory where to store output and results (default: .) 
  #   doc.string:  Documentation string used as a prefix to name result files (default: "GSEA.analysis") 
  #   non.interactive.run: Run in interactive (i.e. R GUI) or batch (R command line) mode (default: F) 
  #   reshuffling.type: Type of permutation reshuffling: "sample.labels" or "gene.labels" (default: "sample.labels") 
  #   nperm: Number of random permutations (default: 1000) 
  #   weighted.score.type: Enrichment correlation-based weighting: 0=no weight (KS), 1=standard weigth, 2 = over-weigth (default: 1) 
  #   nom.p.val.threshold: Significance threshold for nominal p-vals for gene sets (default: -1, no thres) 
  #   fwer.p.val.threshold: Significance threshold for FWER p-vals for gene sets (default: -1, no thres) 
  #   fdr.q.val.threshold: Significance threshold for FDR q-vals for gene sets (default: 0.25) 
  #   topgs: Besides those passing test, number of top scoring gene sets used for detailed reports (default: 10) 
  #   adjust.FDR.q.val: Adjust the FDR q-vals (default: F) 
  #   gs.size.threshold.min: Minimum size (in genes) for database gene sets to be considered (default: 25) 
  #   gs.size.threshold.max: Maximum size (in genes) for database gene sets to be considered (default: 500) 
  #   reverse.sign: Reverse direction of gene list (pos. enrichment becomes negative, etc.) (default: F) 
  #   preproc.type: Preprocessing normalization: 0=none, 1=col(z-score)., 2=col(rank) and row(z-score)., 3=col(rank). (default: 0) 
  #   random.seed: Random number generator seed. (default: 123456) 
  #   perm.type: Permutation type: 0 = unbalanced, 1 = balanced. For experts only (default: 0) 
  #   fraction: Subsampling fraction. Set to 1.0 (no resampling). For experts only (default: 1.0) 
  #   replace: Resampling mode (replacement or not replacement). For experts only (default: F) 
  #   OLD.GSEA: if TRUE compute the OLD GSEA of Mootha et al 2003
  #   use.fast.enrichment.routine: if true it uses a faster version to compute random perm. enrichment "GSEA.EnrichmentScore2"  
  #
  #   Output:
  #    The results of the method are stored in the "output.directory" specified by the user as part of the input parameters. 
  #      The results files are:
  #    - Two tab-separated global result text files (one for each phenotype). These files are labeled according to the doc 
  #      string prefix and the phenotype name from the CLS file: <doc.string>.SUMMARY.RESULTS.REPORT.<phenotype>.txt
  #    - One set of global plots. They include a.- gene list correlation profile, b.- global observed and null densities, c.- heat map 
  #      for the entire sorted dataset, and d.- p-values vs. NES plot. These plots are in a single JPEG file named 
  #      <doc.string>.global.plots.<phenotype>.jpg. When the program is run interactively these plots appear on a window in the R GUI.
  #    - A variable number of tab-separated gene result text files according to how many sets pass any of the significance thresholds 
  #      ("nom.p.val.threshold," "fwer.p.val.threshold," and "fdr.q.val.threshold") and how many are specified in the "topgs" 
  #      parameter. These files are named: <doc.string>.<gene set name>.report.txt. 
  #   - A variable number of gene set plots (one for each gene set report file). These plots include a.- Gene set running enrichment
  #      "mountain" plot, b.- gene set null distribution and c.- heat map for genes in the gene set. These plots are stored in a 
  #      single JPEG file named <doc.string>.<gene set name>.jpg.
  #  The format (columns) for the global result files is as follows.
  #  GS : Gene set name.
  # SIZE : Size of the set in genes.
  # SOURCE : Set definition or source.
  # ES : Enrichment score.
  # NES : Normalized (multiplicative rescaling) normalized enrichment score.
  # NOM p-val : Nominal p-value (from the null distribution of the gene set).
  # FDR q-val: False discovery rate q-values
  # FWER p-val: Family wise error rate p-values.
  # Tag %: Percent of gene set before running enrichment peak.
  # Gene %: Percent of gene list before running enrichment peak.
  # Signal : enrichment signal strength.
  # FDR (median): FDR q-values from the median of the null distributions.
  # glob.p.val: P-value using a global statistic (number of sets above the set's NES).
  # 
  # The rows are sorted by the NES values (from maximum positive or negative NES to minimum)
  # 
  # The format (columns) for the gene set result files is as follows.
  # 
  # #: Gene number in the (sorted) gene set
  # GENE : gene name. For example the probe accession number, gene symbol or the gene identifier gin the dataset.
  # SYMBOL : gene symbol from the gene annotation file.
  # DESC : gene description (title) from the gene annotation file.
  # LIST LOC : location of the gene in the sorted gene list.
  # S2N : signal to noise ratio (correlation) of the gene in the gene list.
  # RES : value of the running enrichment score at the gene location.
  # CORE_ENRICHMENT: is this gene is the "core enrichment" section of the list? Yes or No variable specifying in the gene location is before (positive ES) or after (negative ES) the running enrichment peak.
  # 
  # The rows are sorted by the gene location in the gene list.
  # The function call to GSEA returns a  two element list containing the two global result reports as data frames ($report1, $report2).
  # 
  # results1: Global output report for first phenotype 
  # result2:  Global putput report for second phenotype
  #
  # The Broad Institute
  # SOFTWARE COPYRIGHT NOTICE AGREEMENT
  # This software and its documentation are copyright 2003 by the
  # Broad Institute/Massachusetts Institute of Technology.
  # All rights are reserved.
  #
  # This software is supplied without any warranty or guaranteed support
  # whatsoever. Neither the Broad Institute nor MIT can be responsible for
  # its use, misuse, or functionality.
  
  print(" *** Running GSEA Analysis...")
  
  # Copy input parameters to log file
  
  if (output.directory != "")  {
    
    filename <- paste(output.directory, doc.string, "_params.txt", sep="", collapse="")  
    
    time.string <- as.character(as.POSIXlt(Sys.time(),"GMT"))
    write(paste("Run of GSEA on ", time.string), file=filename)
    
    if (is.data.frame(input.ds)) {
      #      write(paste("input.ds=", quote(input.ds), sep=" "), file=filename, append=T)
    } else {
      write(paste("input.ds=", input.ds, sep=" "), file=filename, append=T)
    }
    if (is.list(input.cls)) {
      #      write(paste("input.cls=", input.cls, sep=" "), file=filename, append=T) 
    } else {
      write(paste("input.cls=", input.cls, sep=" "), file=filename, append=T) 
    }
    if (is.data.frame(gene.ann)) {
      #    write(paste("gene.ann =", gene.ann, sep=" "), file=filename, append=T) 
    } else {
      write(paste("gene.ann =", gene.ann, sep=" "), file=filename, append=T) 
    }
    if (regexpr(pattern=".gmt", gs.db[1]) == -1) {
      #   write(paste("gs.db=", gs.db, sep=" "), file=filename, append=T) 
    } else {
      write(paste("gs.db=", gs.db, sep=" "), file=filename, append=T) 
    }
    if (is.data.frame(gs.ann)) {
      #    write(paste("gene.ann =", gene.ann, sep=" "), file=filename, append=T) 
    } else {
      write(paste("gs.ann =", gs.ann, sep=" "), file=filename, append=T) 
    }
    write(paste("output.directory =", output.directory, sep=" "), file=filename, append=T) 
    write(paste("doc.string = ", doc.string, sep=" "), file=filename, append=T) 
    write(paste("non.interactive.run =", non.interactive.run, sep=" "), file=filename, append=T) 
    write(paste("reshuffling.type =", reshuffling.type, sep=" "), file=filename, append=T) 
    write(paste("nperm =", nperm, sep=" "), file=filename, append=T) 
    write(paste("weighted.score.type =", weighted.score.type, sep=" "), file=filename, append=T) 
    write(paste("nom.p.val.threshold =", nom.p.val.threshold, sep=" "), file=filename, append=T) 
    write(paste("fwer.p.val.threshold =", fwer.p.val.threshold, sep=" "), file=filename, append=T) 
    write(paste("fdr.q.val.threshold =", fdr.q.val.threshold, sep=" "), file=filename, append=T) 
    write(paste("topgs =", topgs, sep=" "), file=filename, append=T)
    write(paste("adjust.FDR.q.val =", adjust.FDR.q.val, sep=" "), file=filename, append=T) 
    write(paste("gs.size.threshold.min =", gs.size.threshold.min, sep=" "), file=filename, append=T) 
    write(paste("gs.size.threshold.max =", gs.size.threshold.max, sep=" "), file=filename, append=T) 
    write(paste("reverse.sign =", reverse.sign, sep=" "), file=filename, append=T) 
    write(paste("preproc.type =", preproc.type, sep=" "), file=filename, append=T) 
    write(paste("random.seed =", random.seed, sep=" "), file=filename, append=T) 
    write(paste("perm.type =", perm.type, sep=" "), file=filename, append=T) 
    write(paste("fraction =", fraction, sep=" "), file=filename, append=T) 
    write(paste("replace =", replace, sep=" "), file=filename, append=T)
  }
  
  # Start of GSEA methodology 
  
  if (.Platform$OS.type == "windows") {
    memory.limit(6000000000)
    memory.limit()
    #      print(c("Start memory size=",  memory.size()))
  }
  
  # Read input data matrix
  
  set.seed(seed=random.seed, kind = NULL)
  adjust.param <- 0.5
  
  gc()
  
  time1 <- proc.time()
  
  if (is.data.frame(input.ds)) {
    dataset <- input.ds
  } else {
    if (regexpr(pattern=".gct", input.ds) == -1) {
      dataset <- GSEA.Res2Frame(filename = input.ds)
    } else {
      #         dataset <- GSEA.Gct2Frame(filename = input.ds)
      dataset <- GSEA.Gct2Frame2(filename = input.ds)
    }
  }
  gene.labels <- row.names(dataset)
  sample.names <- names(dataset)
  A <- data.matrix(dataset)
  dim(A) 
  cols <- length(A[1,])
  rows <- length(A[,1])
  
  # preproc.type control the type of pre-processing: threshold, variation filter, normalization
  
  if (preproc.type == 1) {  # Column normalize (Z-score)
    A <- GSEA.NormalizeCols(A)
  } else if (preproc.type == 2) { # Column (rank) and row (Z-score) normalize 
    for (j in 1:cols) {  # column rank normalization
      A[,j] <- rank(A[,j])
    }
    A <- GSEA.NormalizeRows(A)
  } else if (preproc.type == 3) { # Column (rank) norm.
    for (j in 1:cols) {  # column rank normalization
      A[,j] <- rank(A[,j])
    }
  }
  
  # Read input class vector
  
  if(is.list(input.cls)) {
    CLS <- input.cls
  } else {
    CLS <- GSEA.ReadClsFile(file=input.cls)
  }
  class.labels <- CLS$class.v
  class.phen <- CLS$phen
  
  if (reverse.sign == T) {
    phen1 <- class.phen[2]
    phen2 <- class.phen[1]
  } else {
    phen1 <- class.phen[1]
    phen2 <- class.phen[2]
  }
  
  # sort samples according to phenotype
  
  col.index <- order(class.labels, decreasing=F)
  class.labels <- class.labels[col.index]
  sample.names <- sample.names[col.index]
  for (j in 1:rows) {
    A[j, ] <- A[j, col.index]
  }
  names(A) <- sample.names
  
  # Read input gene set database
  
  if (regexpr(pattern=".gmt", gs.db[1]) == -1) {
    temp <- gs.db
  } else {
    temp <- readLines(gs.db)
  }
  
  max.Ng <- length(temp)
  temp.size.G <- vector(length = max.Ng, mode = "numeric") 
  for (i in 1:max.Ng) {
    temp.size.G[i] <- length(unlist(strsplit(temp[[i]], "\t"))) - 2
  }
  
  max.size.G <- max(temp.size.G)      
  gs <- matrix(rep("null", max.Ng*max.size.G), nrow=max.Ng, ncol= max.size.G)
  temp.names <- vector(length = max.Ng, mode = "character")
  temp.desc <- vector(length = max.Ng, mode = "character")
  gs.count <- 1
  for (i in 1:max.Ng) {
    gene.set.size <- length(unlist(strsplit(temp[[i]], "\t"))) - 2
    gs.line <- noquote(unlist(strsplit(temp[[i]], "\t")))
    gene.set.name <- gs.line[1] 
    gene.set.desc <- gs.line[2] 
    gene.set.tags <- vector(length = gene.set.size, mode = "character")
    for (j in 1:gene.set.size) {
      gene.set.tags[j] <- gs.line[j + 2]
    } 
    existing.set <- is.element(gene.set.tags, gene.labels)
    set.size <- length(existing.set[existing.set == T])
    if ((set.size < gs.size.threshold.min) || (set.size > gs.size.threshold.max)) next
    temp.size.G[gs.count] <- set.size
    gs[gs.count,] <- c(gene.set.tags[existing.set], rep("null", max.size.G - temp.size.G[gs.count]))
    temp.names[gs.count] <- gene.set.name
    temp.desc[gs.count] <- gene.set.desc
    gs.count <- gs.count + 1
  } 
  Ng <- gs.count - 1
  gs.names <- vector(length = Ng, mode = "character")
  gs.desc <- vector(length = Ng, mode = "character")
  size.G <- vector(length = Ng, mode = "numeric") 
  gs.names <- temp.names[1:Ng]
  gs.desc <- temp.desc[1:Ng] 
  size.G <- temp.size.G[1:Ng]
  
  N <- length(A[,1])
  Ns <- length(A[1,])
  
  print(c("Number of genes:", N))
  print(c("Number of Gene Sets:", Ng))
  print(c("Number of samples:", Ns))
  print(c("Original number of Gene Sets:", max.Ng))
  print(c("Maximum gene set size:", max.size.G))
  
  # Read gene and gene set annotations if gene annotation file was provided
  
  all.gene.descs <- vector(length = N, mode ="character") 
  all.gene.symbols <- vector(length = N, mode ="character") 
  all.gs.descs <- vector(length = Ng, mode ="character") 
  
  if (is.data.frame(gene.ann)) {
    temp <- gene.ann
    a.size <- length(temp[,1])
    print(c("Number of gene annotation file entries:", a.size))  
    accs <- as.character(temp[,1])
    locs <- match(gene.labels, accs)
    all.gene.descs <- as.character(temp[locs, "Gene.Title"])
    all.gene.symbols <- as.character(temp[locs, "Gene.Symbol"])
    rm(temp)
  } else  if (gene.ann == "") {
    for (i in 1:N) {
      all.gene.descs[i] <- gene.labels[i]
      all.gene.symbols[i] <- gene.labels[i]
    }
  } else {
    temp <- read.delim(gene.ann, header=T, sep=",", comment.char="", as.is=T)
    a.size <- length(temp[,1])
    print(c("Number of gene annotation file entries:", a.size))  
    accs <- as.character(temp[,1])
    locs <- match(gene.labels, accs)
    all.gene.descs <- as.character(temp[locs, "Gene.Title"])
    all.gene.symbols <- as.character(temp[locs, "Gene.Symbol"])
    rm(temp)
  }
  
  if (is.data.frame(gs.ann)) {
    temp <- gs.ann
    a.size <- length(temp[,1])
    print(c("Number of gene set annotation file entries:", a.size))  
    accs <- as.character(temp[,1])
    locs <- match(gs.names, accs)
    all.gs.descs <- as.character(temp[locs, "SOURCE"])
    rm(temp)
  } else if (gs.ann == "") {
    for (i in 1:Ng) {
      all.gs.descs[i] <- gs.desc[i]
    }
  } else {
    temp <- read.delim(gs.ann, header=T, sep="\t", comment.char="", as.is=T)
    a.size <- length(temp[,1])
    print(c("Number of gene set annotation file entries:", a.size))  
    accs <- as.character(temp[,1])
    locs <- match(gs.names, accs)
    all.gs.descs <- as.character(temp[locs, "SOURCE"])
    rm(temp)
  }
  
  
  Obs.indicator <- matrix(nrow= Ng, ncol=N)
  Obs.RES <- matrix(nrow= Ng, ncol=N)
  
  Obs.ES <- vector(length = Ng, mode = "numeric")
  Obs.arg.ES <- vector(length = Ng, mode = "numeric")
  Obs.ES.norm <- vector(length = Ng, mode = "numeric")
  
  time2 <- proc.time()
  
  # GSEA methodology
  
  # Compute observed and random permutation gene rankings
  
  obs.s2n <- vector(length=N, mode="numeric")
  signal.strength <- vector(length=Ng, mode="numeric")
  tag.frac <- vector(length=Ng, mode="numeric")
  gene.frac <- vector(length=Ng, mode="numeric")
  coherence.ratio <- vector(length=Ng, mode="numeric")
  obs.phi.norm <- matrix(nrow = Ng, ncol = nperm)
  correl.matrix <- matrix(nrow = N, ncol = nperm)
  obs.correl.matrix <- matrix(nrow = N, ncol = nperm)
  order.matrix <- matrix(nrow = N, ncol = nperm)
  obs.order.matrix <- matrix(nrow = N, ncol = nperm)
  
  nperm.per.call <- 100
  n.groups <- nperm %/% nperm.per.call
  n.rem <- nperm %% nperm.per.call
  n.perms <- c(rep(nperm.per.call, n.groups), n.rem)
  n.ends <- cumsum(n.perms)
  n.starts <- n.ends - n.perms + 1
  
  if (n.rem == 0) {
    n.tot <- n.groups
  } else {
    n.tot <- n.groups + 1
  }
  
  for (nk in 1:n.tot) {
    call.nperm <- n.perms[nk]
    
    print(paste("Computing ranked list for actual and permuted phenotypes.......permutations: ", n.starts[nk], "--", n.ends[nk], sep=" "))
    
    O <- GSEA.GeneRanking(A, class.labels, gene.labels, call.nperm, permutation.type = perm.type, sigma.correction = "GeneCluster", fraction=fraction, replace=replace, reverse.sign = reverse.sign)
    gc()
    
    order.matrix[,n.starts[nk]:n.ends[nk]] <- O$order.matrix
    obs.order.matrix[,n.starts[nk]:n.ends[nk]] <- O$obs.order.matrix
    correl.matrix[,n.starts[nk]:n.ends[nk]] <- O$s2n.matrix
    obs.correl.matrix[,n.starts[nk]:n.ends[nk]] <- O$obs.s2n.matrix
    rm(O)
  }
  
  ##median of correlation of each genes in the gene list
  obs.s2n <- apply(obs.correl.matrix, 1, median)  # using median to assign enrichment scores
  obs.index <- order(obs.s2n, decreasing=T)            
  obs.s2n   <- sort(obs.s2n, decreasing=T)            
  
  obs.gene.labels <- gene.labels[obs.index]       
  obs.gene.descs <- all.gene.descs[obs.index]       
  obs.gene.symbols <- all.gene.symbols[obs.index]       
  
  for (r in 1:nperm) {
    correl.matrix[, r] <- correl.matrix[order.matrix[,r], r]
  }
  for (r in 1:nperm) {
    obs.correl.matrix[, r] <- obs.correl.matrix[obs.order.matrix[,r], r]
  }
  
  
  ##gene list ranked!
  gene.list2 <- obs.index
  for (i in 1:Ng) {
    print(paste("Computing observed enrichment for gene set:", i, gs.names[i], sep=" ")) 
    if( gs.names[i]=='DOID:14330'){
      1+1                                                                                      
    }
    gene.set <- gs[i,gs[i,] != "null"]
    gene.set2 <- vector(length=length(gene.set), mode = "numeric")
    gene.set2 <- match(gene.set, gene.labels)
    GSEA.results <- GSEA.EnrichmentScore(gene.list=gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector = obs.s2n)
    
    Obs.ES[i] <- GSEA.results$ES
    Obs.arg.ES[i] <- GSEA.results$arg.ES
    Obs.RES[i,] <- GSEA.results$RES
    Obs.indicator[i,] <- GSEA.results$indicator
    if (Obs.ES[i] >= 0) {  # compute signal strength
      tag.frac[i] <- sum(Obs.indicator[i,1:Obs.arg.ES[i]])/size.G[i]
      gene.frac[i] <- Obs.arg.ES[i]/N
    } else {
      tag.frac[i] <- sum(Obs.indicator[i, Obs.arg.ES[i]:N])/size.G[i]
      gene.frac[i] <- (N - Obs.arg.ES[i] + 1)/N
    }
    signal.strength[i] <- tag.frac[i] * (1 - gene.frac[i]) * (N / (N - size.G[i]))
  }
  
  # Compute enrichment for random permutations 
  
  phi <- matrix(nrow = Ng, ncol = nperm)
  phi.norm <- matrix(nrow = Ng, ncol = nperm)
  obs.phi <- matrix(nrow = Ng, ncol = nperm)
  
  if (reshuffling.type == "sample.labels") { # reshuffling phenotype labels
    for (i in 1:Ng) {
      print(paste("Computing random permutations' enrichment for gene set:", i, gs.names[i], sep=" ")) 
      if( gs.names[i]=='DOID:3856'){
        1+1                                                                                      
      }
      gene.set <- gs[i,gs[i,] != "null"]
      gene.set2 <- vector(length=length(gene.set), mode = "numeric")
      gene.set2 <- match(gene.set, gene.labels)
      for (r in 1:nperm) {
        gene.list2 <- order.matrix[,r]
        if (use.fast.enrichment.routine == F) {
          GSEA.results <- GSEA.EnrichmentScore(gene.list=gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=correl.matrix[, r])   
        } else {
          GSEA.results <- GSEA.EnrichmentScore2(gene.list=gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=correl.matrix[, r])   
        }
        phi[i, r] <- GSEA.results$ES
      }
      if (fraction < 1.0) { # if resampling then compute ES for all observed rankings
        for (r in 1:nperm) {
          obs.gene.list2 <- obs.order.matrix[,r]
          if (use.fast.enrichment.routine == F) {
            GSEA.results <- GSEA.EnrichmentScore(gene.list=obs.gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=obs.correl.matrix[, r]) 
          } else {
            GSEA.results <- GSEA.EnrichmentScore2(gene.list=obs.gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=obs.correl.matrix[, r])
          }
          obs.phi[i, r] <- GSEA.results$ES
        }
      } else { # if no resampling then compute only one column (and fill the others with the same value)
        obs.gene.list2 <- obs.order.matrix[,1]
        if (use.fast.enrichment.routine == F) {
          GSEA.results <- GSEA.EnrichmentScore(gene.list=obs.gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=obs.correl.matrix[, r]) 
        } else {
          GSEA.results <- GSEA.EnrichmentScore2(gene.list=obs.gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=obs.correl.matrix[, r])
        }
        #this is the same as Obs.ES!
        obs.phi[i, 1] <- GSEA.results$ES
        for (r in 2:nperm) {
          obs.phi[i, r] <- obs.phi[i, 1]
        }
      }
      gc()
    }
    
  } else if (reshuffling.type == "gene.labels") { # reshuffling gene labels
    for (i in 1:Ng) {
      gene.set <- gs[i,gs[i,] != "null"]
      gene.set2 <- vector(length=length(gene.set), mode = "numeric")
      gene.set2 <- match(gene.set, gene.labels)
      for (r in 1:nperm) {
        reshuffled.gene.labels <- sample(1:rows)
        GSEA.results <- GSEA.EnrichmentScore(gene.list=reshuffled.gene.labels, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=obs.s2n)   
        phi[i, r] <- GSEA.results$ES
      }
      if (fraction < 1.0) { # if resampling then compute ES for all observed rankings
        for (r in 1:nperm) {
          obs.gene.list2 <- obs.order.matrix[,r]
          GSEA.results <- GSEA.EnrichmentScore(gene.list=obs.gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=obs.correl.matrix[, r])   
          obs.phi[i, r] <- GSEA.results$ES
        }
      } else { # if no resampling then compute only one column (and fill the others with the same value)
        obs.gene.list2 <- obs.order.matrix[,1]
        GSEA.results <- GSEA.EnrichmentScore(gene.list=obs.gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=obs.correl.matrix[, r])   
        obs.phi[i, 1] <- GSEA.results$ES
        for (r in 2:nperm) {
          obs.phi[i, r] <- obs.phi[i, 1]
        }
      }
      gc()
    }
  }
  
  # Compute 3 types of p-values
  
  # Find nominal p-values       
  
  print("Computing nominal p-values...")
  
  p.vals <- matrix(0, nrow = Ng, ncol = 2)
  
  if (OLD.GSEA == F) {
    for (i in 1:Ng) {
      if(gs.names[i] == 'DOID:3856'){
        1+1
      }
      pos.phi <- NULL
      neg.phi <- NULL
      for (j in 1:nperm) {
        if (phi[i, j] >= 0) {
          pos.phi <- c(pos.phi, phi[i, j]) 
        } else {
          neg.phi <- c(neg.phi, phi[i, j]) 
        }
      }
      ES.value <- Obs.ES[i]
      if (ES.value >= 0) {
        p.vals[i, 1] <- signif(sum(pos.phi >= ES.value)/length(pos.phi), digits=10)
      } else {
        p.vals[i, 1] <- signif(sum(neg.phi <= ES.value)/length(neg.phi), digits=10)
      }
    }
  } else {  # For OLD GSEA compute the p-val using positive and negative values in the same histogram
    for (i in 1:Ng) {
      if (Obs.ES[i] >= 0) {
        p.vals[i, 1] <-  sum(phi[i,] >= Obs.ES[i])/length(phi[i,])
        p.vals[i, 1] <-  signif(p.vals[i, 1], digits=5)
      } else {
        p.vals[i, 1] <-  sum(phi[i,] <= Obs.ES[i])/length(phi[i,])
        p.vals[i, 1] <-  signif(p.vals[i, 1], digits=5)
      }
    }
  }
  
  # Find effective size 
  
  erf <- function (x) 
  {
    2 * pnorm(sqrt(2) * x)
  }
  
  KS.mean <- function(N) { # KS mean as a function of set size N
    S <- 0
    for (k in -100:100) {
      if (k == 0) next
      S <- S + 4 * (-1)**(k + 1) * (0.25 * exp(-2 * k * k * N) - sqrt(2 * pi) *  erf(sqrt(2 * N) * k)/(16 * k * sqrt(N)))
    }
    return(abs(S))
  }
  
  # KS.mean.table <- vector(length=5000, mode="numeric")
  
  # for (i in 1:5000) {
  #    KS.mean.table[i] <- KS.mean(i)
  # }
  
  # KS.size <-  vector(length=Ng, mode="numeric")
  
  # Rescaling normalization for each gene set null
  
  print("Computing rescaling normalization for each gene set null...")
  
  if (OLD.GSEA == F) {
    for (i in 1:Ng) {
      if(gs.names[i] == 'DOID:9074'){
        1+1
      }
      pos.phi <- NULL
      neg.phi <- NULL
      for (j in 1:nperm) {
        if (phi[i, j] >= 0) {
          pos.phi <- c(pos.phi, phi[i, j]) 
        } else {
          neg.phi <- c(neg.phi, phi[i, j]) 
        }
      }
      pos.m <- mean(pos.phi)
      neg.m <- mean(abs(neg.phi))
      
      #         if (Obs.ES[i] >= 0) {
      #            KS.size[i] <- which.min(abs(KS.mean.table - pos.m))
      #         } else {
      #            KS.size[i] <- which.min(abs(KS.mean.table - neg.m))
      #         }
      
      #pos.phi <- pos.phi/pos.m
      #neg.phi <- neg.phi/neg.m
      for (j in 1:nperm) {
        if (phi[i, j] >= 0) {
          phi.norm[i, j] <- phi[i, j]/pos.m
        } else {
          phi.norm[i, j] <- phi[i, j]/neg.m
        }
      }
      for (j in 1:nperm) {
        if (obs.phi[i, j] >= 0) {
          obs.phi.norm[i, j] <- obs.phi[i, j]/pos.m
        } else {
          obs.phi.norm[i, j] <- obs.phi[i, j]/neg.m
        }
      }
      if (Obs.ES[i] >= 0) {
        Obs.ES.norm[i] <- Obs.ES[i]/pos.m
      } else {
        Obs.ES.norm[i] <- Obs.ES[i]/neg.m
      }
    }
  } else {  # For OLD GSEA does not normalize using empirical scaling 
    for (i in 1:Ng) {
      for (j in 1:nperm) {
        phi.norm[i, j] <- phi[i, j]/400
      }
      for (j in 1:nperm) {
        obs.phi.norm[i, j] <- obs.phi[i, j]/400
      }
      Obs.ES.norm[i] <- Obs.ES[i]/400
    }
  }
  
  # Save intermedite results
  
  if (save.intermediate.results == T) {
    
    filename <- paste(output.directory, doc.string, ".phi.txt", sep="", collapse="")
    write.table(phi, file = filename, quote=F, col.names= F, row.names=F, sep = "\t")
    
    filename <- paste(output.directory, doc.string, ".obs.phi.txt", sep="", collapse="")
    write.table(obs.phi, file = filename, quote=F, col.names= F, row.names=F, sep = "\t")
    
    filename <- paste(output.directory, doc.string, ".phi.norm.txt", sep="", collapse="")
    write.table(phi.norm, file = filename, quote=F, col.names= F, row.names=F, sep = "\t")
    
    filename <- paste(output.directory, doc.string, ".obs.phi.norm.txt", sep="", collapse="")
    write.table(obs.phi.norm, file = filename, quote=F, col.names= F, row.names=F, sep = "\t")
    
    filename <- paste(output.directory, doc.string, ".Obs.ES.txt", sep="", collapse="")
    write.table(Obs.ES, file = filename, quote=F, col.names= F, row.names=F, sep = "\t")
    
    filename <- paste(output.directory, doc.string, ".Obs.ES.norm.txt", sep="", collapse="")
    write.table(Obs.ES.norm, file = filename, quote=F, col.names= F, row.names=F, sep = "\t")
  }
  #-------------------------------------------------------------------------------------------------------------------  
  #-------------------------------------------------------------------------------------------------------------------  
  #-------------------------------------------------------------------------------------------------------------------  
  #-------------------------------------------------------------------------------------------------------------------  
  # Compute FWER p-vals
  
  print("Computing FWER p-values...")
  
  if (OLD.GSEA == F) {
    max.ES.vals.p <- NULL
    max.ES.vals.n <- NULL
    for (j in 1:nperm) {
      pos.phi <- NULL
      neg.phi <- NULL
      for (i in 1:Ng) {
        if (phi.norm[i, j] >= 0) {
          pos.phi <- c(pos.phi, phi.norm[i, j]) 
        } else {
          neg.phi <- c(neg.phi, phi.norm[i, j]) 
        }
      }
      if (length(pos.phi) > 0) {
        max.ES.vals.p <- c(max.ES.vals.p, max(pos.phi))
      }
      if (length(neg.phi) > 0) {
        max.ES.vals.n <- c(max.ES.vals.n, min(neg.phi))
      }
    }
    for (i in 1:Ng) {
      ES.value <- Obs.ES.norm[i]
      if (Obs.ES.norm[i] >= 0) {
        p.vals[i, 2] <- signif(sum(max.ES.vals.p >= ES.value)/length(max.ES.vals.p), digits=5)
      } else {
        p.vals[i, 2] <- signif(sum(max.ES.vals.n <= ES.value)/length(max.ES.vals.n), digits=5)
      }
    }
  } else {  # For OLD GSEA compute the FWER using positive and negative values in the same histogram
    max.ES.vals <- NULL
    for (j in 1:nperm) {
      max.NES <- max(phi.norm[,j])
      min.NES <- min(phi.norm[,j])
      if (max.NES > - min.NES) {
        max.val <- max.NES
      } else {
        max.val <- min.NES
      }
      max.ES.vals <- c(max.ES.vals, max.val)
    }
    for (i in 1:Ng) {
      if (Obs.ES.norm[i] >= 0) {
        p.vals[i, 2] <- sum(max.ES.vals >= Obs.ES.norm[i])/length(max.ES.vals)
      } else {
        p.vals[i, 2] <- sum(max.ES.vals <= Obs.ES.norm[i])/length(max.ES.vals)
      }
      p.vals[i, 2] <-  signif(p.vals[i, 2], digits=4)
    }
  }
  
  # Compute FDRs 
  
  print("Computing FDR q-values...")
  
  NES <- vector(length=Ng, mode="numeric")
  phi.norm.mean  <- vector(length=Ng, mode="numeric")
  obs.phi.norm.mean  <- vector(length=Ng, mode="numeric")
  phi.norm.median  <- vector(length=Ng, mode="numeric")
  obs.phi.norm.median  <- vector(length=Ng, mode="numeric")
  phi.norm.mean  <- vector(length=Ng, mode="numeric")
  obs.phi.mean  <- vector(length=Ng, mode="numeric")
  FDR.mean <- vector(length=Ng, mode="numeric")
  FDR.median <- vector(length=Ng, mode="numeric")
  phi.norm.median.d <- vector(length=Ng, mode="numeric")
  obs.phi.norm.median.d <- vector(length=Ng, mode="numeric")
  
  Obs.ES.index <- order(Obs.ES.norm, decreasing=T)
  Orig.index <- seq(1, Ng)
  Orig.index <- Orig.index[Obs.ES.index]
  Orig.index <- order(Orig.index, decreasing=F)
  Obs.ES.norm.sorted <- Obs.ES.norm[Obs.ES.index]
  gs.names.sorted <- gs.names[Obs.ES.index]
  
  for (k in 1:Ng) {
    NES[k] <- Obs.ES.norm.sorted[k]
    ES.value <- NES[k]
    count.col <- vector(length=nperm, mode="numeric")
    obs.count.col <- vector(length=nperm, mode="numeric")
    for (i in 1:nperm) {
      phi.vec <- phi.norm[,i]
      obs.phi.vec <- obs.phi.norm[,i]
      if (ES.value >= 0) {
        count.col.norm <- sum(phi.vec >= 0)
        obs.count.col.norm <- sum(obs.phi.vec >= 0)
        count.col[i] <- ifelse(count.col.norm > 0, sum(phi.vec >= ES.value)/count.col.norm, 0)
        obs.count.col[i] <- ifelse(obs.count.col.norm > 0, sum(obs.phi.vec >= ES.value)/obs.count.col.norm, 0)
      } else {
        count.col.norm <- sum(phi.vec < 0)
        obs.count.col.norm <- sum(obs.phi.vec < 0)
        count.col[i] <- ifelse(count.col.norm > 0, sum(phi.vec <= ES.value)/count.col.norm, 0)
        obs.count.col[i] <- ifelse(obs.count.col.norm > 0, sum(obs.phi.vec <= ES.value)/obs.count.col.norm, 0)
      }
    }
    phi.norm.mean[k] <- mean(count.col)
    obs.phi.norm.mean[k] <- mean(obs.count.col)
    phi.norm.median[k] <- median(count.col)
    obs.phi.norm.median[k] <- median(obs.count.col)
    FDR.mean[k] <- ifelse(phi.norm.mean[k]/obs.phi.norm.mean[k] < 1, phi.norm.mean[k]/obs.phi.norm.mean[k], 1)
    FDR.median[k] <- ifelse(phi.norm.median[k]/obs.phi.norm.median[k] < 1, phi.norm.median[k]/obs.phi.norm.median[k], 1)
  }
  
  # adjust q-values
  
  if (adjust.FDR.q.val == T) {
    pos.nes <- length(NES[NES >= 0])
    min.FDR.mean <- FDR.mean[pos.nes]
    min.FDR.median <- FDR.median[pos.nes]
    for (k in seq(pos.nes - 1, 1, -1)) {
      if (FDR.mean[k] < min.FDR.mean) {
        min.FDR.mean <- FDR.mean[k]
      }
      if (min.FDR.mean < FDR.mean[k]) {
        FDR.mean[k] <- min.FDR.mean
      }
    }
    
    neg.nes <- pos.nes + 1
    min.FDR.mean <- FDR.mean[neg.nes]
    min.FDR.median <- FDR.median[neg.nes]
    for (k in seq(neg.nes + 1, Ng)) {
      if (FDR.mean[k] < min.FDR.mean) {
        min.FDR.mean <- FDR.mean[k]
      }
      if (min.FDR.mean < FDR.mean[k]) {
        FDR.mean[k] <- min.FDR.mean
      }
    }
  }
  
  obs.phi.norm.mean.sorted <- obs.phi.norm.mean[Orig.index]
  phi.norm.mean.sorted <- phi.norm.mean[Orig.index]
  FDR.mean.sorted <- FDR.mean[Orig.index]
  FDR.median.sorted <- FDR.median[Orig.index]
  
  #   Compute global statistic
  
  glob.p.vals <- vector(length=Ng, mode="numeric")
  NULL.pass <- vector(length=nperm, mode="numeric")
  OBS.pass <- vector(length=nperm, mode="numeric")
  
  for (k in 1:Ng) {
    NES[k] <- Obs.ES.norm.sorted[k]
    if (NES[k] >= 0) {
      for (i in 1:nperm) {
        NULL.pos <- sum(phi.norm[,i] >= 0)            
        NULL.pass[i] <- ifelse(NULL.pos > 0, sum(phi.norm[,i] >= NES[k])/NULL.pos, 0)
        OBS.pos <- sum(obs.phi.norm[,i] >= 0)
        OBS.pass[i] <- ifelse(OBS.pos > 0, sum(obs.phi.norm[,i] >= NES[k])/OBS.pos, 0)
      }
    } else {
      for (i in 1:nperm) {
        NULL.neg <- sum(phi.norm[,i] < 0)
        NULL.pass[i] <- ifelse(NULL.neg > 0, sum(phi.norm[,i] <= NES[k])/NULL.neg, 0)
        OBS.neg <- sum(obs.phi.norm[,i] < 0)
        OBS.pass[i] <- ifelse(OBS.neg > 0, sum(obs.phi.norm[,i] <= NES[k])/OBS.neg, 0)
      }
    }
    glob.p.vals[k] <- sum(NULL.pass >= mean(OBS.pass))/nperm
  }
  glob.p.vals.sorted <- glob.p.vals[Orig.index]
  
  # Produce results report
  
  print("Producing result tables and plots...")
  
  Obs.ES <- signif(Obs.ES, digits=5)
  Obs.ES.norm <- signif(Obs.ES.norm, digits=5)
  p.vals <- signif(p.vals, digits=4)
  signal.strength <- signif(signal.strength, digits=3)
  tag.frac <- signif(tag.frac, digits=3)
  gene.frac <- signif(gene.frac, digits=3)
  FDR.mean.sorted <- signif(FDR.mean.sorted, digits=5)
  FDR.median.sorted <-  signif(FDR.median.sorted, digits=5)
  glob.p.vals.sorted <- signif(glob.p.vals.sorted, digits=5)
  
  report <- data.frame(cbind(gs.names, size.G, all.gs.descs, Obs.ES, Obs.ES.norm, p.vals[,1], FDR.mean.sorted, p.vals[,2], tag.frac, gene.frac, signal.strength, FDR.median.sorted, glob.p.vals.sorted))
  names(report) <- c("GS", "SIZE", "SOURCE", "ES", "NES", "NOM p-val", "FDR q-val", "FWER p-val", "Tag %", "Gene %", "Signal", "FDR (median)", "glob.p.val")
  #       print(report)
  report2 <- report
  report.index2 <- order(Obs.ES.norm, decreasing=T)
  for (i in 1:Ng) {
    report2[i,] <- report[report.index2[i],]
  }   
  report3 <- report
  report.index3 <- order(Obs.ES.norm, decreasing=F)
  for (i in 1:Ng) {
    report3[i,] <- report[report.index3[i],]
  }   
  phen1.rows <- length(Obs.ES.norm[Obs.ES.norm >= 0])
  phen2.rows <- length(Obs.ES.norm[Obs.ES.norm < 0])
  report.phen1 <- report2[1:phen1.rows,]
  report.phen2 <- report3[1:phen2.rows,]
  
  if (output.directory != "")  {
    if (phen1.rows > 0) {
      filename <- paste(output.directory, doc.string, ".SUMMARY.RESULTS.REPORT.", phen1,".txt", sep="", collapse="")
      write.table(report.phen1, file = filename, quote=F, row.names=F, sep = "\t")
    }
    if (phen2.rows > 0) {
      filename <- paste(output.directory, doc.string, ".SUMMARY.RESULTS.REPORT.", phen2,".txt", sep="", collapse="")
      write.table(report.phen2, file = filename, quote=F, row.names=F, sep = "\t")
    }
  }
  
  # Global plots
  
  if (output.directory != "")  {
    if (non.interactive.run == F) {
      if (.Platform$OS.type == "windows") {
        glob.filename <- paste(output.directory, doc.string, ".global.plots", sep="", collapse="")
        windows(width = 10, height = 10)
      } else if (.Platform$OS.type == "unix") {
        glob.filename <- paste(output.directory, doc.string, ".global.plots.pdf", sep="", collapse="")
        pdf(file=glob.filename, height = 10, width = 10)
      }
    } else {
      if (.Platform$OS.type == "unix") {
        glob.filename <- paste(output.directory, doc.string, ".global.plots.pdf", sep="", collapse="")
        pdf(file=glob.filename, height = 10, width = 10)
      } else if (.Platform$OS.type == "windows") {
        glob.filename <- paste(output.directory, doc.string, ".global.plots.pdf", sep="", collapse="")
        pdf(file=glob.filename, height = 10, width = 10)
      }
    }
  }
  
  nf <- layout(matrix(c(1,2,3,4), 2, 2, byrow=T), c(1,1), c(1,1), TRUE)
  
  # plot S2N correlation profile
  
  location <- 1:N
  max.corr <- max(obs.s2n)
  min.corr <- min(obs.s2n)
  
  x <- plot(location, obs.s2n, ylab = "Signal to Noise Ratio (S2N)", xlab = "Gene List Location", main = "Gene List Correlation (S2N) Profile", type = "l", lwd = 2, cex = 0.9, col = 1)            
  for (i in seq(1, N, 20)) {
    lines(c(i, i), c(0, obs.s2n[i]), lwd = 3, cex = 0.9, col = colors()[12]) # shading of correlation plot
  }
  x <- points(location, obs.s2n, type = "l", lwd = 2, cex = 0.9, col = 1)            
  lines(c(1, N), c(0, 0), lwd = 2, lty = 1, cex = 0.9, col = 1) # zero correlation horizontal line
  temp <- order(abs(obs.s2n), decreasing=T)
  arg.correl <- temp[N]
  lines(c(arg.correl, arg.correl), c(min.corr, 0.7*max.corr), lwd = 2, lty = 3, cex = 0.9, col = 1) # zero correlation vertical line
  
  area.bias <- signif(100*(sum(obs.s2n[1:arg.correl]) + sum(obs.s2n[arg.correl:N]))/sum(abs(obs.s2n[1:N])), digits=3)
  area.phen <- ifelse(area.bias >= 0, phen1, phen2)
  delta.string <- paste("Corr. Area Bias to \"", area.phen, "\" =", abs(area.bias), "\\%", sep="", collapse="")
  zero.crossing.string <- paste("Zero Crossing at location ", arg.correl, " (",  signif(100*arg.correl/N, digits=3), " \\%)")
  leg.txt <- c(delta.string, zero.crossing.string)
  legend(x=N/10, y=max.corr, bty="n", bg = "white", legend=leg.txt, cex = 0.9)
  
  leg.txt <- paste("\"", phen1, "\" ", sep="", collapse="")
  text(x=1, y=-0.05*max.corr, adj = c(0, 1), labels=leg.txt, cex = 0.9)
  
  leg.txt <- paste("\"", phen2, "\" ", sep="", collapse="")
  text(x=N, y=0.05*max.corr, adj = c(1, 0), labels=leg.txt, cex = 0.9)
  
  if (Ng > 1) { # make these plots only if there are multiple gene sets.
    
    # compute plots of actual (weighted) null and observed
    
    phi.densities.pos <- matrix(0, nrow=512, ncol=nperm)
    phi.densities.neg <- matrix(0, nrow=512, ncol=nperm)
    obs.phi.densities.pos <- matrix(0, nrow=512, ncol=nperm)
    obs.phi.densities.neg <- matrix(0, nrow=512, ncol=nperm)
    phi.density.mean.pos <- vector(length=512, mode = "numeric")
    phi.density.mean.neg <- vector(length=512, mode = "numeric")
    obs.phi.density.mean.pos <- vector(length=512, mode = "numeric")
    obs.phi.density.mean.neg <- vector(length=512, mode = "numeric")
    phi.density.median.pos <- vector(length=512, mode = "numeric")
    phi.density.median.neg <- vector(length=512, mode = "numeric")
    obs.phi.density.median.pos <- vector(length=512, mode = "numeric")
    obs.phi.density.median.neg <- vector(length=512, mode = "numeric")
    x.coor.pos <-  vector(length=512, mode = "numeric")
    x.coor.neg <-  vector(length=512, mode = "numeric")
    
    for (i in 1:nperm) {
      pos.phi <- phi.norm[phi.norm[, i] >= 0, i]
      if (length(pos.phi) > 2) {
        temp <- density(pos.phi, adjust=adjust.param, n = 512, from=0, to=3.5)
      } else {
        temp <- list(x = 3.5*(seq(1, 512) - 1)/512, y = rep(0.001, 512))
      }
      phi.densities.pos[, i] <- temp$y
      norm.factor <- sum(phi.densities.pos[, i])
      phi.densities.pos[, i] <- phi.densities.pos[, i]/norm.factor
      if (i == 1) {
        x.coor.pos <- temp$x
      }
      
      neg.phi <- phi.norm[phi.norm[, i] < 0, i]
      if (length(neg.phi) > 2) {
        temp <- density(neg.phi, adjust=adjust.param, n = 512, from=-3.5, to=0)
      } else {
        temp <- list(x = 3.5*(seq(1, 512) - 1)/512, y = rep(0.001, 512))
      }
      phi.densities.neg[, i] <- temp$y
      norm.factor <- sum(phi.densities.neg[, i])
      phi.densities.neg[, i] <- phi.densities.neg[, i]/norm.factor
      if (i == 1) {
        x.coor.neg <- temp$x
      }
      pos.phi <- obs.phi.norm[obs.phi.norm[, i] >= 0, i]
      if (length(pos.phi) > 2) {
        temp <- density(pos.phi, adjust=adjust.param, n = 512, from=0, to=3.5)
      } else {
        temp <- list(x = 3.5*(seq(1, 512) - 1)/512, y = rep(0.001, 512))
      }
      obs.phi.densities.pos[, i] <- temp$y
      norm.factor <- sum(obs.phi.densities.pos[, i])
      obs.phi.densities.pos[, i] <- obs.phi.densities.pos[, i]/norm.factor
      
      neg.phi <- obs.phi.norm[obs.phi.norm[, i] < 0, i]
      if (length(neg.phi)> 2) {  
        temp <- density(neg.phi, adjust=adjust.param, n = 512, from=-3.5, to=0)
      } else {
        temp <- list(x = 3.5*(seq(1, 512) - 1)/512, y = rep(0.001, 512))
      }
      obs.phi.densities.neg[, i] <- temp$y
      norm.factor <- sum(obs.phi.densities.neg[, i])
      obs.phi.densities.neg[, i] <- obs.phi.densities.neg[, i]/norm.factor
      
    }
    phi.density.mean.pos <- apply(phi.densities.pos, 1, mean)
    phi.density.mean.neg <- apply(phi.densities.neg, 1, mean)
    
    obs.phi.density.mean.pos <- apply(obs.phi.densities.pos, 1, mean)
    obs.phi.density.mean.neg <- apply(obs.phi.densities.neg, 1, mean)
    
    phi.density.median.pos <- apply(phi.densities.pos, 1, median)
    phi.density.median.neg <- apply(phi.densities.neg, 1, median)
    
    obs.phi.density.median.pos <- apply(obs.phi.densities.pos, 1, median)
    obs.phi.density.median.neg <- apply(obs.phi.densities.neg, 1, median)
    
    x <- c(x.coor.neg, x.coor.pos)
    x.plot.range <- range(x)
    y1 <- c(phi.density.mean.neg, phi.density.mean.pos)
    y2 <- c(obs.phi.density.mean.neg, obs.phi.density.mean.pos)
    y.plot.range <- c(-0.3*max(c(y1, y2)),  max(c(y1, y2)))
    
    print(c(y.plot.range, max(c(y1, y2)), max(y1), max(y2)))
    
    plot(x, y1, xlim = x.plot.range, ylim = 1.5*y.plot.range, type = "l", lwd = 2, col = 2, xlab = "NES", ylab = "P(NES)", main = "Global Observed and Null Densities (Area Normalized)")
    
    y1.point <- y1[seq(1, length(x), 2)]
    y2.point <- y2[seq(2, length(x), 2)]
    x1.point <- x[seq(1, length(x), 2)]
    x2.point <- x[seq(2, length(x), 2)]
    
    #     for (i in 1:length(x1.point)) {
    #       lines(c(x1.point[i], x1.point[i]), c(0, y1.point[i]), lwd = 3, cex = 0.9, col = colors()[555]) # shading 
    #     }
    #
    #     for (i in 1:length(x2.point)) {
    #       lines(c(x2.point[i], x2.point[i]), c(0, y2.point[i]), lwd = 3, cex = 0.9, col = colors()[29]) # shading 
    #     }
    
    points(x, y1, type = "l", lwd = 2, col = colors()[555])
    points(x, y2, type = "l", lwd = 2, col = colors()[29])
    
    for (i in 1:Ng) {
      col <- ifelse(Obs.ES.norm[i] > 0, 2, 3) 
      lines(c(Obs.ES.norm[i], Obs.ES.norm[i]), c(-0.2*max(c(y1, y2)), 0), lwd = 1, lty = 1, col = 1)
    }
    leg.txt <- paste("Neg. ES: \"", phen2, " \" ", sep="", collapse="")
    text(x=x.plot.range[1], y=-0.25*max(c(y1, y2)), adj = c(0, 1), labels=leg.txt, cex = 0.9)
    leg.txt <- paste(" Pos. ES: \"", phen1, "\" ", sep="", collapse="")
    text(x=x.plot.range[2], y=-0.25*max(c(y1, y2)), adj = c(1, 1), labels=leg.txt, cex = 0.9)
    
    leg.txt <- c("Null Density", "Observed Density", "Observed NES values")
    c.vec <- c(colors()[555], colors()[29], 1)
    lty.vec <- c(1, 1, 1)
    lwd.vec <- c(2, 2, 2)
    legend(x=0, y=1.5*y.plot.range[2], bty="n", bg = "white", legend=leg.txt, lty = lty.vec, lwd = lwd.vec, col = c.vec, cex = 0.9)
    
    B <- A[obs.index,]
    if (N > 300) {
      C <- rbind(B[1:100,], rep(0, Ns), rep(0, Ns), B[(floor(N/2) - 50 + 1):(floor(N/2) + 50),], rep(0, Ns), rep(0, Ns), B[(N - 100 + 1):N,])
    } 
    rm(B)
    GSEA.HeatMapPlot(V = C, col.labels = class.labels, col.classes = class.phen, main = "Heat Map for Genes in Dataset")
    
    # p-vals plot
    nom.p.vals <- p.vals[Obs.ES.index,1]
    FWER.p.vals <- p.vals[Obs.ES.index,2]
    plot.range <- 1.25*range(NES)
    plot(NES, FDR.mean, ylim = c(0, 1), xlim = plot.range, col = 1, bg = 1, type="p", pch = 22, cex = 0.75, xlab = "NES", main = "p-values vs. NES", ylab ="p-val/q-val")
    points(NES, nom.p.vals, type = "p", col = 2, bg = 2, pch = 22, cex = 0.75)
    points(NES, FWER.p.vals, type = "p", col = colors()[577], bg = colors()[577], pch = 22, cex = 0.75)
    leg.txt <- c("Nominal p-value", "FWER p-value", "FDR q-value")
    c.vec <- c(2, colors()[577], 1)
    pch.vec <- c(22, 22, 22)
    legend(x=-0.5, y=0.5, bty="n", bg = "white", legend=leg.txt, pch = pch.vec, col = c.vec, pt.bg = c.vec, cex = 0.9)
    lines(c(min(NES), max(NES)), c(nom.p.val.threshold, nom.p.val.threshold), lwd = 1, lty = 2, col = 2) 
    lines(c(min(NES), max(NES)), c(fwer.p.val.threshold, fwer.p.val.threshold), lwd = 1, lty = 2, col = colors()[577]) 
    lines(c(min(NES), max(NES)), c(fdr.q.val.threshold, fdr.q.val.threshold), lwd = 1, lty = 2, col = 1) 
    
    if (non.interactive.run == F) {  
      if (.Platform$OS.type == "windows") {
        savePlot(filename = glob.filename, type ="jpeg", device = dev.cur())
      } else if (.Platform$OS.type == "unix") {
        dev.off()
      }
    } else {
      dev.off()
    }
    
  } # if Ng > 1
  
  #----------------------------------------------------------------------------
  # Produce report for each gene set passing the nominal, FWER or FDR test or the top topgs in each side
  
  if (topgs > floor(Ng/2)) {
    topgs <- floor(Ng/2)
  }
  
  for (i in 1:Ng) {
    if ((p.vals[i, 1] <= nom.p.val.threshold) ||
          (p.vals[i, 2] <= fwer.p.val.threshold) ||
          (FDR.mean.sorted[i] <= fdr.q.val.threshold) || 
          (is.element(i, c(Obs.ES.index[1:topgs], Obs.ES.index[(Ng - topgs + 1): Ng])))) {
      
      #  produce report per gene set
      
      kk <- 1
      gene.number <- vector(length = size.G[i], mode = "character")
      gene.names <- vector(length = size.G[i], mode = "character")
      gene.symbols <- vector(length = size.G[i], mode = "character")
      gene.descs <- vector(length = size.G[i], mode = "character")
      gene.list.loc <- vector(length = size.G[i], mode = "numeric")
      core.enrichment <- vector(length = size.G[i], mode = "character")
      gene.s2n <- vector(length = size.G[i], mode = "numeric")
      gene.RES <- vector(length = size.G[i], mode = "numeric")
      rank.list <- seq(1, N)
      
      if (Obs.ES[i] >= 0) {
        set.k <- seq(1, N, 1)
        phen.tag <- phen1
        loc <- match(i, Obs.ES.index)
      } else {
        set.k <- seq(N, 1, -1)
        phen.tag <- phen2
        loc <- Ng - match(i, Obs.ES.index) + 1
      }
      
      for (k in set.k) {
        if (Obs.indicator[i, k] == 1) {
          gene.number[kk] <- kk
          gene.names[kk] <- obs.gene.labels[k]
          gene.symbols[kk] <- substr(obs.gene.symbols[k], 1, 15)
          gene.descs[kk] <- substr(obs.gene.descs[k], 1, 40)
          gene.list.loc[kk] <- k
          gene.s2n[kk] <- signif(obs.s2n[k], digits=3)
          gene.RES[kk] <- signif(Obs.RES[i, k], digits = 3)
          if (Obs.ES[i] >= 0) {
            core.enrichment[kk] <- ifelse(gene.list.loc[kk] <= Obs.arg.ES[i], "YES", "NO")
          } else {
            core.enrichment[kk] <- ifelse(gene.list.loc[kk] > Obs.arg.ES[i], "YES", "NO")
          }
          kk <- kk + 1
        }
      }
      
      gene.report <- data.frame(cbind(gene.number, gene.names, gene.symbols, gene.descs, gene.list.loc, gene.s2n, gene.RES, core.enrichment))
      names(gene.report) <- c("#", "GENE", "SYMBOL", "DESC", "LIST LOC", "S2N", "RES", "CORE_ENRICHMENT")
      
      #       print(gene.report)
      
      if (output.directory != "")  {
        
        filename <- paste(output.directory, doc.string, ".", gs.names[i], ".report.", phen.tag, ".", loc, ".txt", sep="", collapse="")
        write.table(gene.report, file = filename, quote=F, row.names=F, sep = "\t")
        
        if (non.interactive.run == F) {
          if (.Platform$OS.type == "windows") {
            gs.filename <- paste(output.directory, doc.string, ".", gs.names[i], ".plot.", phen.tag, ".", loc, sep="", collapse="")
            windows(width = 14, height = 6)
          } else if (.Platform$OS.type == "unix") {
            gs.filename <- paste(output.directory, doc.string, ".", gs.names[i], ".plot.", phen.tag, ".", loc, ".pdf", sep="", collapse="")
            pdf(file=gs.filename, height = 6, width = 14)
          }
        } else {
          if (.Platform$OS.type == "unix") {
            gs.filename <- paste(output.directory, doc.string, ".", gs.names[i], ".plot.", phen.tag, ".", loc, ".pdf", sep="", collapse="")
            pdf(file=gs.filename, height = 6, width = 14)
          } else if (.Platform$OS.type == "windows") {
            gs.filename <- paste(output.directory, doc.string, ".", gs.names[i], ".plot.", phen.tag, ".", loc, ".pdf", sep="", collapse="")
            pdf(file=gs.filename, height = 6, width = 14)
          }
        }
        
      }
      
      nf <- layout(matrix(c(1,2,3), 1, 3, byrow=T), 1, c(1, 1, 1), TRUE)
      ind <- 1:N
      min.RES <- min(Obs.RES[i,])
      max.RES <- max(Obs.RES[i,])
      if (max.RES < 0.3) max.RES <- 0.3
      if (min.RES > -0.3) min.RES <- -0.3
      delta <- (max.RES - min.RES)*0.50
      min.plot <- min.RES - 2*delta
      max.plot <- max.RES
      max.corr <- max(obs.s2n)
      min.corr <- min(obs.s2n)
      Obs.correl.vector.norm <- (obs.s2n - min.corr)/(max.corr - min.corr)*1.25*delta + min.plot
      zero.corr.line <- (- min.corr/(max.corr - min.corr))*1.25*delta + min.plot
      col <- ifelse(Obs.ES[i] > 0, 2, 4)
      
      # Running enrichment plot
      
      sub.string <- paste("Number of genes: ", N, " (in list), ", size.G[i], " (in gene set)", sep = "", collapse="")
      
      main.string <- paste("Gene Set ", i, ":", gs.names[i])
      plot(ind, Obs.RES[i,], main = main.string, sub = sub.string, xlab = "Gene List Index", ylab = "Running Enrichment Score (RES)", xlim=c(1, N), ylim=c(min.plot, max.plot), type = "l", lwd = 2, cex = 1, col = col)
      for (j in seq(1, N, 20)) {
        lines(c(j, j), c(zero.corr.line, Obs.correl.vector.norm[j]), lwd = 1, cex = 1, col = colors()[12]) # shading of correlation plot
      }
      lines(c(1, N), c(0, 0), lwd = 1, lty = 2, cex = 1, col = 1) # zero RES line
      lines(c(Obs.arg.ES[i], Obs.arg.ES[i]), c(min.plot, max.plot), lwd = 1, lty = 3, cex = 1, col = col) # max enrichment vertical line
      for (j in 1:N) {
        if (Obs.indicator[i, j] == 1) {
          lines(c(j, j), c(min.plot + 1.25*delta, min.plot + 1.75*delta), lwd = 1, lty = 1, cex = 1, col = 1)  # enrichment tags
        }
      }
      lines(ind, Obs.correl.vector.norm, type = "l", lwd = 1, cex = 1, col = 1)
      lines(c(1, N), c(zero.corr.line, zero.corr.line), lwd = 1, lty = 1, cex = 1, col = 1) # zero correlation horizontal line
      temp <- order(abs(obs.s2n), decreasing=T)
      arg.correl <- temp[N]
      lines(c(arg.correl, arg.correl), c(min.plot, max.plot), lwd = 1, lty = 3, cex = 1, col = 3) # zero crossing correlation vertical line
      
      leg.txt <- paste("\"", phen1, "\" ", sep="", collapse="")
      text(x=1, y=min.plot, adj = c(0, 0), labels=leg.txt, cex = 1.0)
      
      leg.txt <- paste("\"", phen2, "\" ", sep="", collapse="")
      text(x=N, y=min.plot, adj = c(1, 0), labels=leg.txt, cex = 1.0)
      
      adjx <- ifelse(Obs.ES[i] > 0, 0, 1)
      
      leg.txt <- paste("Peak at ", Obs.arg.ES[i], sep="", collapse="")
      text(x=Obs.arg.ES[i], y=min.plot + 1.8*delta, adj = c(adjx, 0), labels=leg.txt, cex = 1.0)
      
      leg.txt <- paste("Zero crossing at ", arg.correl, sep="", collapse="")
      text(x=arg.correl, y=min.plot + 1.95*delta, adj = c(adjx, 0), labels=leg.txt, cex = 1.0)
      
      # nominal p-val histogram
      
      sub.string <- paste("ES =", signif(Obs.ES[i], digits = 3), " NES =", signif(Obs.ES.norm[i], digits=3), "Nom. p-val=", signif(p.vals[i, 1], digits = 3),"FWER=", signif(p.vals[i, 2], digits = 3), "FDR=", signif(FDR.mean.sorted[i], digits = 3))
      temp <- density(phi[i,], adjust=adjust.param)
      x.plot.range <- range(temp$x)
      y.plot.range <- c(-0.125*max(temp$y), 1.5*max(temp$y))
      plot(temp$x, temp$y, type = "l", sub = sub.string, xlim = x.plot.range, ylim = y.plot.range, lwd = 2, col = 2, main = "Gene Set Null Distribution", xlab = "ES", ylab="P(ES)")
      x.loc <- which.min(abs(temp$x - Obs.ES[i]))
      lines(c(Obs.ES[i], Obs.ES[i]), c(0, temp$y[x.loc]), lwd = 2, lty = 1, cex = 1, col = 1)
      lines(x.plot.range, c(0, 0), lwd = 1, lty = 1, cex = 1, col = 1)
      
      leg.txt <- c("Gene Set Null Density", "Observed Gene Set ES value")
      c.vec <- c(2, 1)
      lty.vec <- c(1, 1)
      lwd.vec <- c(2, 2)
      legend(x=-0.2, y=y.plot.range[2], bty="n", bg = "white", legend=leg.txt, lty = lty.vec, lwd = lwd.vec, col = c.vec, cex = 1.0)
      
      leg.txt <- paste("Neg. ES \"", phen2, "\" ", sep="", collapse="")
      text(x=x.plot.range[1], y=-0.1*max(temp$y), adj = c(0, 0), labels=leg.txt, cex = 1.0)
      leg.txt <- paste(" Pos. ES: \"", phen1, "\" ", sep="", collapse="")
      text(x=x.plot.range[2], y=-0.1*max(temp$y), adj = c(1, 0), labels=leg.txt, cex = 1.0)
      
      # create pinkogram for each gene set
      
      kk <- 1
      
      pinko <- matrix(0, nrow = size.G[i], ncol = cols)
      pinko.gene.names <- vector(length = size.G[i], mode = "character")
      for (k in 1:rows) {
        if (Obs.indicator[i, k] == 1) {
          pinko[kk,] <- A[obs.index[k],]
          pinko.gene.names[kk] <- obs.gene.symbols[k]
          kk <- kk + 1
        }
      }
      GSEA.HeatMapPlot(V = pinko, row.names = pinko.gene.names, col.labels = class.labels, col.classes = class.phen, col.names = sample.names, main =" Heat Map for Genes in Gene Set", xlab=" ", ylab=" ")
      
      if (non.interactive.run == F) {  
        if (.Platform$OS.type == "windows") {
          savePlot(filename = gs.filename, type ="jpeg", device = dev.cur())
        } else if (.Platform$OS.type == "unix") {
          dev.off()
        }
      } else {
        dev.off()
      }
      
    } # if p.vals thres
    
  } # loop over gene sets
  
  
  return(list(report1 = report.phen1, report2 = report.phen2))
  
}  # end of definition of GSEA.analysis


GSEA.write.gct <- function (gct, filename) 
{
  f <- file(filename, "w")
  cat("#1.2", "\n", file = f, append = TRUE, sep = "")
  cat(dim(gct)[1], "\t", dim(gct)[2], "\n", file = f, append = TRUE, sep = "")
  cat("Name", "\t", file = f, append = TRUE, sep = "")
  cat("Description", file = f, append = TRUE, sep = "")
  names <- names(gct)
  cat("\t", names[1], file = f, append = TRUE, sep = "")
  for (j in 2:length(names)) {
    cat("\t", names[j], file = f, append = TRUE, sep = "")
  }
  cat("\n", file = f, append = TRUE, sep = "\t")
  oldWarn <- options(warn = -1)
  m <- matrix(nrow = dim(gct)[1], ncol = dim(gct)[2] +  2)
  m[, 1] <- row.names(gct)
  m[, 2] <- row.names(gct)
  index <- 3
  for (i in 1:dim(gct)[2]) {
    m[, index] <- gct[, i]
    index <- index + 1
  }
  write.table(m, file = f, append = TRUE, quote = FALSE, sep = "\t", eol = "\n", col.names = FALSE, row.names = FALSE)
  close(f)
  options(warn = 0)
  return(gct)
}


GSEA.ConsPlot <- function(V, col.names, main = " ", sub = " ", xlab=" ", ylab=" ") {
  
  # Plots a heatmap plot of a consensus matrix
  
  cols <- length(V[1,])
  B <- matrix(0, nrow=cols, ncol=cols)
  max.val <- max(V)
  min.val <- min(V)
  for (i in 1:cols) {
    for (j in 1:cols) {
      k <- cols - i + 1
      B[k, j] <-  max.val - V[i, j] + min.val
    }
  }
  
  
  
  #     col.map <- c(rainbow(100, s = 1.0, v = 0.75, start = 0.0, end = 0.75, gamma = 1.5), "#BBBBBB", "#333333", "#FFFFFF")
  col.map <- rev(c("#0000FF", "#4040FF", "#7070FF", "#8888FF", "#A9A9FF", "#D5D5FF", "#EEE5EE", "#FFAADA", "#FF9DB0", "#FF7080", "#FF5A5A", "#FF4040", "#FF0D1D"))
  
  #     max.size <- max(nchar(col.names))
  par(mar = c(5, 15, 15, 5))
  image(1:cols, 1:cols, t(B), col = col.map, axes=FALSE, main=main, sub=sub, xlab= xlab, ylab=ylab)
  
  for (i in 1:cols) {
    col.names[i]  <- substr(col.names[i], 1, 25)
  }
  col.names2 <- rev(col.names)
  
  size.col.char <- ifelse(cols < 15, 1, sqrt(15/cols))
  
  axis(2, at=1:cols, labels=col.names2, adj= 0.5, tick=FALSE, las = 1, cex.axis=size.col.char, font.axis=1, line=-1)
  axis(3, at=1:cols, labels=col.names, adj= 1, tick=FALSE, las = 3, cex.axis=size.col.char, font.axis=1, line=-1)
  
  return()
}

GSEA.HeatMapPlot2 <- function(V, row.names = "NA", col.names = "NA", main = " ", sub = " ", xlab=" ", ylab=" ", color.map = "default") {
  #
  # Plots a heatmap of a matrix
  
  n.rows <- length(V[,1])
  n.cols <- length(V[1,])
  
  if (color.map == "default") {
    color.map <- rev(rainbow(100, s = 1.0, v = 0.75, start = 0.0, end = 0.75, gamma = 1.5))
  }
  
  heatm <- matrix(0, nrow = n.rows, ncol = n.cols)
  heatm[1:n.rows,] <- V[seq(n.rows, 1, -1),]
  
  par(mar = c(7, 15, 5, 5))
  image(1:n.cols, 1:n.rows, t(heatm), col=color.map, axes=FALSE, main=main, sub = sub, xlab= xlab, ylab=ylab)
  
  if (length(row.names) > 1) {
    size.row.char <- ifelse(n.rows < 15, 1, sqrt(15/n.rows))
    size.col.char <- ifelse(n.cols < 15, 1, sqrt(10/n.cols))
    #            size.col.char <- ifelse(n.cols < 2.5, 1, sqrt(2.5/n.cols))
    for (i in 1:n.rows) {
      row.names[i] <- substr(row.names[i], 1, 40)
    }
    row.names <- row.names[seq(n.rows, 1, -1)]
    axis(2, at=1:n.rows, labels=row.names, adj= 0.5, tick=FALSE, las = 1, cex.axis=size.row.char, font.axis=1, line=-1)
  }
  
  if (length(col.names) > 1) {
    axis(1, at=1:n.cols, labels=col.names, tick=FALSE, las = 3, cex.axis=size.col.char, font.axis=2, line=-1)
  }
  
  return()
}


GSEA.Analyze.Sets <- function(
  directory,
  topgs = "",
  non.interactive.run = F,
  height = 12,
  width = 17) {
  
  file.list <- list.files(directory)
  files <- file.list[regexpr(pattern = "\\.report\\.", file.list) > 1]
  max.sets <- length(files)
  
  set.table <- matrix(nrow = max.sets, ncol = 5)
  
  for (i in 1:max.sets) {
    temp1 <-  strsplit(files[i], split="\\.report\\.")
    temp2 <-  strsplit(temp1[[1]][1], split="\\.")
    s <- length(temp2[[1]])
    prefix.name <- paste(temp2[[1]][1:(s-1)], sep="", collapse="")
    set.name <- temp2[[1]][s]
    temp3 <-  strsplit(temp1[[1]][2], split="\\.")
    phenotype <- temp3[[1]][1]
    seq.number <- temp3[[1]][2]
    dataset <- paste(temp2[[1]][1:(s-1)], sep="", collapse="\\.")
    
    set.table[i, 1] <- files[i]
    
    set.table[i, 3] <- phenotype
    set.table[i, 4] <- as.numeric(seq.number)
    set.table[i, 5] <- dataset
    
    #      set.table[i, 2] <- paste(set.name, dataset, sep ="", collapse="")
    set.table[i, 2] <- substr(set.name, 1, 20) 
  }
  
  print(c("set name=", prefix.name))
  doc.string <- prefix.name
  
  set.table <- noquote(set.table)
  phen.order <- order(set.table[, 3], decreasing = T)
  set.table <- set.table[phen.order,]
  phen1 <- names(table(set.table[,3]))[1]
  phen2 <- names(table(set.table[,3]))[2]
  set.table.phen1 <- set.table[set.table[,3] == phen1,]
  set.table.phen2 <- set.table[set.table[,3] == phen2,]
  
  seq.order <- order(as.numeric(set.table.phen1[, 4]), decreasing = F)
  set.table.phen1 <- set.table.phen1[seq.order,]
  seq.order <- order(as.numeric(set.table.phen2[, 4]), decreasing = F)
  set.table.phen2 <- set.table.phen2[seq.order,]
  
  #   max.sets.phen1 <- length(set.table.phen1[,1])
  #   max.sets.phen2 <- length(set.table.phen2[,1])
  
  if (topgs == "") {
    max.sets.phen1 <- length(set.table.phen1[,1])
    max.sets.phen2 <- length(set.table.phen2[,1])
  } else {
    max.sets.phen1 <- ifelse(topgs > length(set.table.phen1[,1]), length(set.table.phen1[,1]), topgs) 
    max.sets.phen2 <- ifelse(topgs > length(set.table.phen2[,1]), length(set.table.phen2[,1]), topgs)
  }
  
  # Analysis for phen1
  
  leading.lists <- NULL
  for (i in 1:max.sets.phen1) {
    inputfile <- paste(directory, set.table.phen1[i, 1], sep="", collapse="")
    gene.set <- read.table(file=inputfile, sep="\t", header=T, comment.char="", as.is=T)
    leading.set <- as.vector(gene.set[gene.set[,"CORE_ENRICHMENT"] == "YES", "SYMBOL"])
    leading.lists <- c(leading.lists, list(leading.set))
    if (i == 1) {
      all.leading.genes <- leading.set 
    } else{
      all.leading.genes <- union(all.leading.genes, leading.set)
    }
  }
  max.genes <- length(all.leading.genes)
  M <- matrix(0, nrow=max.sets.phen1, ncol=max.genes)
  for (i in 1:max.sets.phen1) {
    M[i,] <- sign(match(all.leading.genes, as.vector(leading.lists[[i]]), nomatch=0))   # notice that the sign is 0 (no tag) or 1 (tag) 
  }
  
  Inter <- matrix(0, nrow=max.sets.phen1, ncol=max.sets.phen1)
  for (i in 1:max.sets.phen1) {
    for (j in 1:max.sets.phen1) {
      Inter[i, j] <- length(intersect(leading.lists[[i]], leading.lists[[j]]))/length(union(leading.lists[[i]], leading.lists[[j]]))
    }
  }
  
  Itable <- data.frame(Inter)
  names(Itable) <- set.table.phen1[1:max.sets.phen1, 2]
  row.names(Itable) <- set.table.phen1[1:max.sets.phen1, 2]
  
  if (non.interactive.run == F) {
    if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.overlap.", phen1, sep="", collapse="")
      windows(height = width, width = width)
    } else if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.overlap.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = width, width = width)
    }
  } else {
    if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.overlap.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = width, width = width)
    } else if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.overlap.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = width, width = width)
    }
  }
  
  GSEA.ConsPlot(Itable, col.names = set.table.phen1[1:max.sets.phen1, 2], main = " ", sub=paste("Leading Subsets Overlap ", doc.string, " - ", phen1, sep=""), xlab=" ", ylab=" ")
  
  if (non.interactive.run == F) {  
    if (.Platform$OS.type == "windows") {
      savePlot(filename = filename, type ="jpeg", device = dev.cur())
    } else if (.Platform$OS.type == "unix") {
      dev.off()
    }
  } else {
    dev.off()
  }
  
  # Save leading subsets in a GCT file
  
  D.phen1 <- data.frame(M)
  names(D.phen1) <- all.leading.genes
  row.names(D.phen1) <- set.table.phen1[1:max.sets.phen1, 2]
  output <- paste(directory, doc.string, ".leading.genes.", phen1, ".gct", sep="")
  GSEA.write.gct(D.phen1, filename=output)
  
  # Save leading subsets as a single gene set in a .gmt file
  
  row.header <- paste(doc.string, ".all.leading.genes.", phen1, sep="")
  output.line <- paste(all.leading.genes, sep="\t", collapse="\t")
  output.line <- paste(row.header, row.header, output.line, sep="\t", collapse="")
  output <- paste(directory, doc.string, ".all.leading.genes.", phen1, ".gmt", sep="")
  write(noquote(output.line), file = output, ncolumns = length(output.line))
  
  if (non.interactive.run == F) {
    if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.assignment.", phen1, sep="", collapse="")
      windows(height = height, width = width)
    } else if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.assignment.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    }
  } else {
    if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.assignment.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    } else if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.assignment.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    }
  }
  
  cmap <-  c("#AAAAFF", "#111166")
  GSEA.HeatMapPlot2(V = data.matrix(D.phen1), row.names = row.names(D.phen1), col.names = names(D.phen1), main = "Leading Subsets Assignment", sub = paste(doc.string, " - ", phen1, sep=""), xlab=" ", ylab=" ", color.map = cmap) 
  
  if (non.interactive.run == F) {  
    if (.Platform$OS.type == "windows") {
      savePlot(filename = filename, type ="jpeg", device = dev.cur())
    } else if (.Platform$OS.type == "unix") {
      dev.off()
    }
  } else {
    dev.off()
  }
  
  DT1.phen1 <- data.matrix(t(D.phen1))
  DT2.phen1 <- data.frame(DT1.phen1)
  names(DT2.phen1) <- set.table.phen1[1:max.sets.phen1, 2]
  row.names(DT2.phen1) <- all.leading.genes
  #   GSEA.write.gct(DT2.phen1, filename=outputfile2.phen1)
  
  # Analysis for phen2
  
  leading.lists <- NULL
  for (i in 1:max.sets.phen2) {
    inputfile <- paste(directory, set.table.phen2[i, 1], sep="", collapse="")
    gene.set <- read.table(file=inputfile, sep="\t", header=T, comment.char="", as.is=T)
    leading.set <- as.vector(gene.set[gene.set[,"CORE_ENRICHMENT"] == "YES", "SYMBOL"])
    leading.lists <- c(leading.lists, list(leading.set))
    if (i == 1) {
      all.leading.genes <- leading.set 
    } else{
      all.leading.genes <- union(all.leading.genes, leading.set)
    }
  }
  max.genes <- length(all.leading.genes)
  M <- matrix(0, nrow=max.sets.phen2, ncol=max.genes)
  for (i in 1:max.sets.phen2) {
    M[i,] <- sign(match(all.leading.genes, as.vector(leading.lists[[i]]), nomatch=0))   # notice that the sign is 0 (no tag) or 1 (tag) 
  }
  
  Inter <- matrix(0, nrow=max.sets.phen2, ncol=max.sets.phen2)
  for (i in 1:max.sets.phen2) {
    for (j in 1:max.sets.phen2) {
      Inter[i, j] <- length(intersect(leading.lists[[i]], leading.lists[[j]]))/length(union(leading.lists[[i]], leading.lists[[j]]))
    }
  }
  
  Itable <- data.frame(Inter)
  names(Itable) <- set.table.phen2[1:max.sets.phen2, 2]
  row.names(Itable) <- set.table.phen2[1:max.sets.phen2, 2]
  
  if (non.interactive.run == F) {
    if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.overlap.", phen2, sep="", collapse="")
      windows(height = width, width = width)
    } else if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.overlap.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = width, width = width)
    }
  } else {
    if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.overlap.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = width, width = width)
    } else if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.overlap.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = width, width = width)
    }
  }
  
  GSEA.ConsPlot(Itable, col.names = set.table.phen2[1:max.sets.phen2, 2], main = " ", sub=paste("Leading Subsets Overlap ", doc.string, " - ", phen2, sep=""), xlab=" ", ylab=" ")
  
  if (non.interactive.run == F) {  
    if (.Platform$OS.type == "windows") {
      savePlot(filename = filename, type ="jpeg", device = dev.cur())
    } else if (.Platform$OS.type == "unix") {
      dev.off()
    }
  } else {
    dev.off()
  }
  
  # Save leading subsets in a GCT file
  
  D.phen2 <- data.frame(M)
  names(D.phen2) <- all.leading.genes
  row.names(D.phen2) <- set.table.phen2[1:max.sets.phen2, 2]
  output <- paste(directory, doc.string, ".leading.genes.", phen2, ".gct", sep="")
  GSEA.write.gct(D.phen2, filename=output)
  
  # Save primary subsets as a single gene set in a .gmt file
  
  row.header <- paste(doc.string, ".all.leading.genes.", phen2, sep="")
  output.line <- paste(all.leading.genes, sep="\t", collapse="\t")
  output.line <- paste(row.header, row.header, output.line, sep="\t", collapse="")
  output <- paste(directory, doc.string, ".all.leading.genes.", phen2, ".gmt", sep="")
  write(noquote(output.line), file = output, ncolumns = length(output.line))
  
  if (non.interactive.run == F) {
    if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.assignment.", phen2, sep="", collapse="")
      windows(height = height, width = width)
    } else if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.assignment.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    }
  } else {
    if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.assignment.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    } else if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.assignment.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    }
  }
  
  cmap <-  c("#AAAAFF", "#111166")
  GSEA.HeatMapPlot2(V = data.matrix(D.phen2), row.names = row.names(D.phen2), col.names = names(D.phen2), main = "Leading Subsets Assignment", sub = paste(doc.string, " - ", phen2, sep=""), xlab=" ", ylab=" ", color.map = cmap) 
  
  if (non.interactive.run == F) {  
    if (.Platform$OS.type == "windows") {
      savePlot(filename = filename, type ="jpeg", device = dev.cur())
    } else if (.Platform$OS.type == "unix") {
      dev.off()
    }
  } else {
    dev.off()
  }
  
  DT1.phen2 <- data.matrix(t(D.phen2))
  DT2.phen2 <- data.frame(DT1.phen2)
  names(DT2.phen2) <- set.table.phen2[1:max.sets.phen2, 2]
  row.names(DT2.phen2) <- all.leading.genes
  #   GSEA.write.gct(DT2.phen2, filename=outputfile2.phen2)
  
  # Resort columns and rows for phen1
  
  A <- data.matrix(D.phen1)
  A.row.names <- row.names(D.phen1)
  A.names <- names(D.phen1)
  
  # Max.genes
  
  #   init <- 1
  #   for (k in 1:max.sets.phen1) { 
  #      end <- which.max(cumsum(A[k,]))
  #      if (end - init > 1) {
  #         B <- A[,init:end]
  #         B.names <- A.names[init:end]
  #        dist.matrix <- dist(t(B))
  #         HC <- hclust(dist.matrix, method="average")
  ##         B <- B[,HC$order] + 0.2*(k %% 2)
  #        B <- B[,HC$order] 
  #         A[,init:end] <- B
  #         A.names[init:end] <- B.names[HC$order]
  #         init <- end + 1
  #     }
  #   }
  
  #   windows(width=14, height=10)
  #   GSEA.HeatMapPlot2(V = A, row.names = A.row.names, col.names = A.names, sub = "  ", main = paste("Primary Sets Assignment - ", doc.string, " - ", phen1, sep=""), xlab=" ", ylab=" ") 
  
  dist.matrix <- dist(t(A))
  HC <- hclust(dist.matrix, method="average")
  A <- A[, HC$order]
  A.names <- A.names[HC$order]
  
  dist.matrix <- dist(A)
  HC <- hclust(dist.matrix, method="average")
  A <- A[HC$order,]
  A.row.names <- A.row.names[HC$order]
  
  if (non.interactive.run == F) {
    if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen1, sep="", collapse="")
      windows(height = height, width = width)
    } else if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    }
  } else {
    if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    } else if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen1, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    }
  }
  
  
  
  cmap <-  c("#AAAAFF", "#111166")
  #   GSEA.HeatMapPlot2(V = A, row.names = A.row.names, col.names = A.names, main = "Leading Subsets Assignment (clustered)", sub = paste(doc.string, " - ", phen1, sep=""), xlab=" ", ylab=" ", color.map = cmap) 
  
  GSEA.HeatMapPlot2(V = t(A), row.names = A.names, col.names = A.row.names, main = "Leading Subsets Assignment (clustered)", sub = paste(doc.string, " - ", phen1, sep=""), xlab=" ", ylab=" ", color.map = cmap) 
  
  text.filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen1, ".txt", sep="", collapse="")
  line.list <- c("Gene", A.row.names)
  line.header <- paste(line.list, collapse="\t")
  line.length <- length(A.row.names) + 1
  write(line.header, file = text.filename, ncolumns = line.length)
  write.table(t(A), file=text.filename, append = T, quote=F, col.names= F, row.names=T, sep = "\t")
  
  if (non.interactive.run == F) {  
    if (.Platform$OS.type == "windows") {
      savePlot(filename = filename, type ="jpeg", device = dev.cur())
    } else if (.Platform$OS.type == "unix") {
      dev.off()
    }
  } else {
    dev.off()
  }
  
  
  
  
  
  
  # resort columns and rows for phen2
  
  A <- data.matrix(D.phen2)
  A.row.names <- row.names(D.phen2)
  A.names <- names(D.phen2)
  
  # Max.genes
  
  #   init <- 1
  #   for (k in 1:max.sets.phen2) { 
  #      end <- which.max(cumsum(A[k,]))
  #      if (end - init > 1) {
  #         B <- A[,init:end]
  #         B.names <- A.names[init:end]
  #         dist.matrix <- dist(t(B))
  #         HC <- hclust(dist.matrix, method="average")
  ##         B <- B[,HC$order] + 0.2*(k %% 2)
  #        B <- B[,HC$order] 
  #         A[,init:end] <- B
  #         A.names[init:end] <- B.names[HC$order]
  #         init <- end + 1
  #     }
  #   }
  
  #  windows(width=14, height=10)
  #  GESA.HeatMapPlot2(V = A, row.names = A.row.names, col.names = A.names, sub = "  ", main = paste("Primary Sets Assignment - ", doc.string, " - ", phen2, sep=""), xlab=" ", ylab=" ") 
  
  dist.matrix <- dist(t(A))
  HC <- hclust(dist.matrix, method="average")
  A <- A[, HC$order]
  A.names <- A.names[HC$order]
  
  dist.matrix <- dist(A)
  HC <- hclust(dist.matrix, method="average")
  A <- A[HC$order,]
  A.row.names <- A.row.names[HC$order]
  
  if (non.interactive.run == F) {
    if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen2, sep="", collapse="")
      windows(height = height, width = width)
    } else if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    }
  } else {
    if (.Platform$OS.type == "unix") {
      filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    } else if (.Platform$OS.type == "windows") {
      filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen2, ".pdf", sep="", collapse="")
      pdf(file=filename, height = height, width = width)
    }
  }
  
  cmap <-  c("#AAAAFF", "#111166")
  
  #   GSEA.HeatMapPlot2(V = A, row.names = A.row.names, col.names = A.names, main = "Leading Subsets Assignment (clustered)", sub = paste(doc.string, " - ", phen2, sep=""), xlab=" ", ylab=" ", color.map = cmap) 
  GSEA.HeatMapPlot2(V = t(A), row.names =A.names , col.names = A.row.names, main = "Leading Subsets Assignment (clustered)", sub = paste(doc.string, " - ", phen2, sep=""), xlab=" ", ylab=" ", color.map = cmap) 
  
  text.filename <- paste(directory, doc.string, ".leading.assignment.clustered.", phen2, ".txt", sep="", collapse="")
  line.list <- c("Gene", A.row.names)
  line.header <- paste(line.list, collapse="\t")
  line.length <- length(A.row.names) + 1
  write(line.header, file = text.filename, ncolumns = line.length)
  write.table(t(A), file=text.filename, append = T, quote=F, col.names= F, row.names=T, sep = "\t")
  
  if (non.interactive.run == F) {  
    if (.Platform$OS.type == "windows") {
      savePlot(filename = filename, type ="jpeg", device = dev.cur())
    } else if (.Platform$OS.type == "unix") {
      dev.off()
    }
  } else {
    dev.off()
  }
  
}








# end of auxiliary functions

# ----------------------------------------------------------------------------------------
# Main GSEA Analysis Function that implements the entire methodology



elim<-function(mg,GO2geneID,sig.p=99){
  
  nodeLevel <- buildLevels(mg)
  levelsLookUp <- nodeLevel$level2nodes
  
  ## we use a lookup table to search for nodes that have were significant
  sigNodes.LookUP <- new.env(hash = TRUE, parent = emptyenv())
  
  ## hash table for the genes that we eliminate for each node
  ## we store the genes that we want to eliminate
  elimGenes.LookUP <- new.env(hash = TRUE, parent = emptyenv())
  
  ## hash table to store the result
  sigList <- new.env(hash = TRUE, parent = emptyenv())
  
  counter=0
  total=nodeLevel$noOfNodes
  for(i in nodeLevel$noOfLevels:1) {
    currNodes.names <- get(as.character(i), envir = as.environment(levelsLookUp), mode = 'character')
    ##children.currNodes <- adj(goDAG.r2l, currNodes.names)
    currAnno <- GO2geneID[currNodes.names]
    
    .num.elimGenes <- length(unique(unlist(as.list(elimGenes.LookUP))))
    cat(paste("\n\t Level ", i, ":\t", length(currNodes.names),
              " nodes to be scored\t(", .num.elimGenes, " eliminated genes) ",paste(currNodes.names,collapse='\t'),"\n",sep =""))
    
    for(termID in currNodes.names) {
      if(termID=='DOID:0050890'){
        1+1                                                                                      
      }
      counter=counter+1
      cat(paste(counter," / ",total,"\n",sep=''))
      ## remove the genes from the term, if there are
      if(exists(termID, envir = elimGenes.LookUP, mode = "character"))
        GO2geneID[[termID]]=setdiff(GO2geneID[[termID]],get(termID, envir = elimGenes.LookUP, mode = 'character'))
      
      if(length(GO2geneID[[termID]])==0)
        next
      
      gs.db=paste(termID,terms[[termID]],paste(GO2geneID[[termID]],collapse="\t"),sep="\t")
      
      
      ## run the test and store the result (the p-value)
      result<-gsea(gs.db)
      if(length(result$p)==0)
        next
      ## if we have a significant GO term 
      if(result$p <= sig.p) {
        ## we mark it
        assign(termID, result$p, envir = sigNodes.LookUP)
        
        ## we set the genes that we want to eliminate from the all ancestors
        elimGenesID <- currAnno[[termID]]
        
        ## we look for the ancestors
        ancestors <- findAllParentNodes(mg,termID)
        
        oldElimGenesID <- mget(ancestors, envir = elimGenes.LookUP,
                               mode = 'character', ifnotfound = list(NA))
        
        ## add the new genesID to the ancestors
        newElimGenesID <- lapply(oldElimGenesID,
                                 function(termGenes) {
                                   aux <- union(termGenes, elimGenesID)
                                   return(aux[!is.na(aux)])
                                 })
        
        
        ## update the lookUp table
        if(length(newElimGenesID) > 0)
          multiassign(names(newElimGenesID), newElimGenesID, envir = elimGenes.LookUP)
      }
    }
  }
  
  list('elimGenes.LookUP'=as.list.environment(elimGenes.LookUP),'sigNodes.LookUP'=as.list.environment(sigNodes.LookUP))
  
}






GSEA.elim <- function(
  input.ds="/home/xin/Downloads/GSEA-P-R/Datasets/Leukemia.gct", 
  input.cls = "/home/xin/Downloads/GSEA-P-R/Datasets/Leukemia.cls",  
  gene.ann = "", 
  gs.db = "/home/xin/Downloads/GSEA-P-R/GeneSetDatabases/C2.gmt",  
  Term2geneID.symbol,
  Terms,
  graph,
  sig.p=0.5,
  gs.ann = "",
  output.directory = "/home/xin/Downloads/GSEA-P-R/TEST/", 
  doc.string = "GSEA.analysis", 
  non.interactive.run = F, 
  reshuffling.type = "sample.labels", 
  nperm = 10, 
  weighted.score.type = 1, 
  nom.p.val.threshold = -1, 
  fwer.p.val.threshold = -1, 
  fdr.q.val.threshold = 0.25, 
  topgs = 20,
  adjust.FDR.q.val = F, 
  gs.size.threshold.min = 10, 
  gs.size.threshold.max = 800, 
  reverse.sign = F, 
  preproc.type = 0, 
  random.seed = 3338, 
  perm.type = 0, 
  fraction = 1.0, 
  replace = F,
  save.intermediate.results = F,
  OLD.GSEA = F,
  use.fast.enrichment.routine = F) {
  
  print(" *** Running GSEA Analysis...")
  
  if (.Platform$OS.type == "windows") {
    memory.limit(6000000000)
    memory.limit()
    #      print(c("Start memory size=",  memory.size()))
  }
  
  # Read input data matrix
  
  set.seed(seed=random.seed, kind = NULL)
  adjust.param <- 0.5
  
  gc()
  
  time1 <- proc.time()
  
  if (is.data.frame(input.ds)) {
    dataset <- input.ds
  } else {
    if (regexpr(pattern=".gct", input.ds) == -1) {
      dataset <- GSEA.Res2Frame(filename = input.ds)
    } else {
      #         dataset <- GSEA.Gct2Frame(filename = input.ds)
      dataset <- GSEA.Gct2Frame2(filename = input.ds)
    }
  }
  gene.labels <- row.names(dataset)
  sample.names <- names(dataset)
  A <- data.matrix(dataset)
  dim(A) 
  cols <- length(A[1,])
  rows <- length(A[,1])
  
  # preproc.type control the type of pre-processing: threshold, variation filter, normalization
  
  if (preproc.type == 1) {  # Column normalize (Z-score)
    A <- GSEA.NormalizeCols(A)
  } else if (preproc.type == 2) { # Column (rank) and row (Z-score) normalize 
    for (j in 1:cols) {  # column rank normalization
      A[,j] <- rank(A[,j])
    }
    A <- GSEA.NormalizeRows(A)
  } else if (preproc.type == 3) { # Column (rank) norm.
    for (j in 1:cols) {  # column rank normalization
      A[,j] <- rank(A[,j])
    }
  }
  
  # Read input class vector
  
  if(is.list(input.cls)) {
    CLS <- input.cls
  } else {
    CLS <- GSEA.ReadClsFile(file=input.cls)
  }
  class.labels <- CLS$class.v
  class.phen <- CLS$phen
  
  if (reverse.sign == T) {
    phen1 <- class.phen[2]
    phen2 <- class.phen[1]
  } else {
    phen1 <- class.phen[1]
    phen2 <- class.phen[2]
  }
  
  # sort samples according to phenotype
  
  col.index <- order(class.labels, decreasing=F)
  class.labels <- class.labels[col.index]
  sample.names <- sample.names[col.index]
  for (j in 1:rows) {
    A[j, ] <- A[j, col.index]
  }
  names(A) <- sample.names
  
  # Read input gene set database
  if (regexpr(pattern=".gmt", gs.db[1]) == -1) {
    temp <- gs.db
    max.Ng <- length(temp)
    temp.size.G <- vector(length = max.Ng, mode = "numeric") 
    for (i in 1:max.Ng) {
      temp.size.G[i] <- length(unlist(strsplit(temp[[i]], "\t"))) - 2
    }
  } else {
    temp <- readLines(gs.db)
    max.Ng <- length(temp)
    temp.size.G <- vector(length = max.Ng, mode = "numeric") 
    for (i in 1:max.Ng) {
      temp.size.G[i] <- length(temp[[i]])
    }  
  }
  
  
  max.size.G <- max(temp.size.G)      
  gs <- matrix(rep("null", max.Ng*max.size.G), nrow=max.Ng, ncol= max.size.G)
  temp.names <- vector(length = max.Ng, mode = "character")
  temp.desc <- vector(length = max.Ng, mode = "character")
  gs.count <- 1
  for (i in 1:max.Ng) {
    gene.set.size <- length(temp[[i]])
    gene.set.name <- names(temp[i])
    gene.set.desc <- Terms[[gene.set.name]]
    gene.set.tags <- vector(length = gene.set.size, mode = "character")
    gene.set.tags <-temp[[i]]
    
    existing.set <- is.element(gene.set.tags, gene.labels)
    set.size <- length(existing.set[existing.set == T])
    #print(set.size)
    if ((set.size < gs.size.threshold.min) || (set.size > gs.size.threshold.max)) next
    temp.size.G[gs.count] <- set.size
    gs[gs.count,] <- c(gene.set.tags[existing.set], rep("null", max.size.G - temp.size.G[gs.count]))
    temp.names[gs.count] <- gene.set.name
    temp.desc[gs.count] <- gene.set.desc
    gs.count <- gs.count + 1
  } 
  Ng <- gs.count - 1
  gs.names <- vector(length = Ng, mode = "character")
  gs.desc <- vector(length = Ng, mode = "character")
  size.G <- vector(length = Ng, mode = "numeric") 
  gs.names <- temp.names[1:Ng]
  gs.desc <- temp.desc[1:Ng] 
  size.G <- temp.size.G[1:Ng]
  
  N <- length(A[,1])
  Ns <- length(A[1,])
  
  #   print(c("Number of genes:", N))
  #   print(c("Number of Gene Sets:", Ng))
  #   print(c("Number of samples:", Ns))
  #   print(c("Original number of Gene Sets:", max.Ng))
  #   print(c("Maximum gene set size:", max.size.G))
  
  # Read gene and gene set annotations if gene annotation file was provided
  
  all.gene.descs <- vector(length = N, mode ="character") 
  all.gene.symbols <- vector(length = N, mode ="character") 
  all.gs.descs <- vector(length = Ng, mode ="character") 
  
  if (is.data.frame(gene.ann)) {
    temp <- gene.ann
    a.size <- length(temp[,1])
    print(c("Number of gene annotation file entries:", a.size))  
    accs <- as.character(temp[,1])
    locs <- match(gene.labels, accs)
    all.gene.descs <- as.character(temp[locs, "Gene.Title"])
    all.gene.symbols <- as.character(temp[locs, "Gene.Symbol"])
    rm(temp)
  } else  if (gene.ann == "") {
    for (i in 1:N) {
      all.gene.descs[i] <- gene.labels[i]
      all.gene.symbols[i] <- gene.labels[i]
    }
  } else {
    temp <- read.delim(gene.ann, header=T, sep=",", comment.char="", as.is=T)
    a.size <- length(temp[,1])
    print(c("Number of gene annotation file entries:", a.size))  
    accs <- as.character(temp[,1])
    locs <- match(gene.labels, accs)
    all.gene.descs <- as.character(temp[locs, "Gene.Title"])
    all.gene.symbols <- as.character(temp[locs, "Gene.Symbol"])
    rm(temp)
  }
  
  if (is.data.frame(gs.ann)) {
    temp <- gs.ann
    a.size <- length(temp[,1])
    print(c("Number of gene set annotation file entries:", a.size))  
    accs <- as.character(temp[,1])
    locs <- match(gs.names, accs)
    all.gs.descs <- as.character(temp[locs, "SOURCE"])
    rm(temp)
  } else if (gs.ann == "") {
    for (i in 1:Ng) {
      all.gs.descs[i] <- gs.desc[i]
    }
  } else {
    temp <- read.delim(gs.ann, header=T, sep="\t", comment.char="", as.is=T)
    a.size <- length(temp[,1])
    print(c("Number of gene set annotation file entries:", a.size))  
    accs <- as.character(temp[,1])
    locs <- match(gs.names, accs)
    all.gs.descs <- as.character(temp[locs, "SOURCE"])
    rm(temp)
  }
  
  
  Obs.indicator <- matrix(nrow= Ng, ncol=N)
  Obs.RES <- matrix(nrow= Ng, ncol=N)
  
  Obs.ES <- vector(length = Ng, mode = "numeric")
  Obs.arg.ES <- vector(length = Ng, mode = "numeric")
  Obs.ES.norm <- vector(length = Ng, mode = "numeric")
  
  time2 <- proc.time()
  
  # GSEA methodology
  
  # Compute observed and random permutation gene rankings
  
  obs.s2n <- vector(length=N, mode="numeric")
  signal.strength <- vector(length=Ng, mode="numeric")
  tag.frac <- vector(length=Ng, mode="numeric")
  gene.frac <- vector(length=Ng, mode="numeric")
  coherence.ratio <- vector(length=Ng, mode="numeric")
  obs.phi.norm <- matrix(nrow = Ng, ncol = nperm)
  correl.matrix <- matrix(nrow = N, ncol = nperm)
  obs.correl.matrix <- matrix(nrow = N, ncol = nperm)
  order.matrix <- matrix(nrow = N, ncol = nperm)
  obs.order.matrix <- matrix(nrow = N, ncol = nperm)
  
  nperm.per.call <- 100
  n.groups <- nperm %/% nperm.per.call
  n.rem <- nperm %% nperm.per.call
  n.perms <- c(rep(nperm.per.call, n.groups), n.rem)
  n.ends <- cumsum(n.perms)
  n.starts <- n.ends - n.perms + 1
  
  if (n.rem == 0) {
    n.tot <- n.groups
  } else {
    n.tot <- n.groups + 1
  }
  
  for (nk in 1:n.tot) {
    call.nperm <- n.perms[nk]
    
    print(paste("Computing ranked list for actual and permuted phenotypes.......permutations: ", n.starts[nk], "--", n.ends[nk], sep=" "))
    
    O <- GSEA.GeneRanking(A, class.labels, gene.labels, call.nperm, permutation.type = perm.type, sigma.correction = "GeneCluster", fraction=fraction, replace=replace, reverse.sign = reverse.sign)
    gc()
    
    order.matrix[,n.starts[nk]:n.ends[nk]] <- O$order.matrix
    obs.order.matrix[,n.starts[nk]:n.ends[nk]] <- O$obs.order.matrix
    correl.matrix[,n.starts[nk]:n.ends[nk]] <- O$s2n.matrix
    obs.correl.matrix[,n.starts[nk]:n.ends[nk]] <- O$obs.s2n.matrix
    rm(O)
  }
  
  ##median of correlation of each genes in the gene list
  obs.s2n <- apply(obs.correl.matrix, 1, median)  # using median to assign enrichment scores
  obs.index <- order(obs.s2n, decreasing=T)            
  obs.s2n   <- sort(obs.s2n, decreasing=T)            
  
  obs.gene.labels <- gene.labels[obs.index]       
  obs.gene.descs <- all.gene.descs[obs.index]       
  obs.gene.symbols <- all.gene.symbols[obs.index]       
  
  for (r in 1:nperm) {
    correl.matrix[, r] <- correl.matrix[order.matrix[,r], r]
  }
  for (r in 1:nperm) {
    obs.correl.matrix[, r] <- obs.correl.matrix[obs.order.matrix[,r], r]
  }
  
  
  ##gene list ranked!
  gene.list2 <- obs.index
  #####elim 
  message("elim....")
  nodeLevel <- buildLevels(graph)
  levelsLookUp <- nodeLevel$level2nodes
  
  ## we use a lookup table to search for nodes that have were significant
  sigNodes.LookUP <- new.env(hash = TRUE, parent = emptyenv())
  
  ## hash table for the genes that we eliminate for each node
  ## we store the genes that we want to eliminate
  elimGenes.LookUP <- new.env(hash = TRUE, parent = emptyenv())
  
  ## hash table to store the result
  sigList <- new.env(hash = TRUE, parent = emptyenv())
  
  counter=0
  total=length(which(V(graph)$name %in% gs.names))
  for(i in nodeLevel$noOfLevels:1) {
    currNodes.names <- get(as.character(i), envir = as.environment(levelsLookUp), mode = 'character')
    ##children.currNodes <- adj(goDAG.r2l, currNodes.names)
    ##remove nodes that did not pass the previous step
    currNodes.names=intersect(currNodes.names,gs.names)
    currAnno <- GO2geneID.symbol[currNodes.names]
    
    .num.elimGenes <- length(unique(unlist(as.list(elimGenes.LookUP))))
    cat(paste("\n\t Level ", i, ":\t", length(currNodes.names),
              " nodes to be scored\t(", .num.elimGenes, " eliminated genes) ",paste(currNodes.names,collapse='\t'),"\n",sep =""))
    
    for(termID in currNodes.names) {
      counter=counter+1
      cat(paste(counter," / ",total,"\n",sep=''))
      message(paste("Computing observed enrichment for gene set:", termID, sep=" ")) 
      
      
      if(termID=='DOID:14330'){
        1+1                                                                                      
      }
      
      ## remove the genes from the term, if there are
      if(exists(termID, envir = elimGenes.LookUP, mode = "character"))
        GO2geneID.symbol[[termID]]=setdiff(GO2geneID.symbol[[termID]],get(termID, envir = elimGenes.LookUP, mode = 'character'))
      
      if(length(GO2geneID.symbol[[termID]])==0)
        next
      
      
      ##gene list ranked!
      gene.list2 <- obs.index
      
      gene.set <- GO2geneID.symbol[[termID]]
      gene.set2 <- vector(length=length(gene.set), mode = "numeric")
      gene.set2 <- match(gene.set, gene.labels)
      gene.set2 <- gene.set2[!is.na(gene.set2)]
      GSEA.results <- GSEA.EnrichmentScore(gene.list=gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector = obs.s2n)
      
      Obs.ES <- GSEA.results$ES
      Obs.arg.ES <- GSEA.results$arg.ES
      Obs.RES <- GSEA.results$RES
      Obs.indicator <- GSEA.results$indicator
      
      phi <- vector(length=nperm)
      phi.norm <- vector(length=nperm)
      obs.phi <- vector(length=nperm)
      
      if (reshuffling.type == "sample.labels") { # reshuffling phenotype labels
        message(paste("Computing random permutations' enrichment for gene set:", termID, sep=" ")) 
        gene.set <- GO2geneID.symbol[[termID]]
        gene.set2 <- vector(length=length(gene.set), mode = "numeric")
        gene.set2 <- match(gene.set, gene.labels)
        gene.set2<- gene.set2[!is.na(gene.set2)]
        for (r in 1:nperm) {
          gene.list2 <- order.matrix[,r]
          if (use.fast.enrichment.routine == F) {
            GSEA.results <- GSEA.EnrichmentScore(gene.list=gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=correl.matrix[, r])   
          } else {
            GSEA.results <- GSEA.EnrichmentScore2(gene.list=gene.list2, gene.set=gene.set2, weighted.score.type=weighted.score.type, correl.vector=correl.matrix[, r])   
          }
          phi[r] <- GSEA.results$ES
        }
      }
      
      # Compute 3 types of p-values
      
      # Find nominal p-values       
      
      message("Computing nominal p-values...")
      
      p.vals <- vector(length=1)
      pos.phi <- NULL
      neg.phi <- NULL
      for (i in 1:nperm) {
        if (phi[i] >= 0) {
          pos.phi <- c(pos.phi, phi[i]) 
        } else {
          neg.phi <- c(neg.phi, phi[i]) 
        }
      }
      ES.value <- Obs.ES
      if (ES.value >= 0) {
        p.vals <- signif(sum(pos.phi >= ES.value)/length(pos.phi), digits=10)
      } else {
        p.vals <- signif(sum(neg.phi <= ES.value)/length(neg.phi), digits=10)
      }
      
      
      
      ## if we have a significant GO term 
      if(p.vals <= sig.p) {
        message(paste("We found a significant(",p.vals,") term [",termID,"],",length(currAnno[[termID]]),"genes will be eliminate from its ancestors." ))
        message("-------------------------------------------------------------------------")
        ## we mark it
        assign(termID, p.vals, envir = sigNodes.LookUP)
        
        ## we set the genes that we want to eliminate from the all ancestors
        elimGenesID <- currAnno[[termID]]
        
        ## we look for the ancestors
        ancestors <- findAllParentNodes(graph,termID)
        
        oldElimGenesID <- mget(ancestors, envir = elimGenes.LookUP,
                               mode = 'character', ifnotfound = list(NA))
        
        ## add the new genesID to the ancestors
        newElimGenesID <- lapply(oldElimGenesID,
                                 function(termGenes) {
                                   aux <- union(termGenes, elimGenesID)
                                   return(aux[!is.na(aux)])
                                 })
        
        
        ## update the lookUp table
        if(length(newElimGenesID) > 0)
          multiassign(names(newElimGenesID), newElimGenesID, envir = elimGenes.LookUP)
      }else{
        message(paste("not a sigificnt term. [",p.vals,"]."))
      }
    }
  }
  
  
  gs.db=NULL
  terms<-Term(ONTTERM)
  for(i in names(GO2geneID.symbol)){
    s=paste(i,terms[[i]],paste(GO2geneID.symbol[[i]],collapse="\t"),sep="\t")
    gs.db=c(gs.db,s)
    s=''
  }
  
  GSEA(                                                                    # Input/Output Files :-------------------------------------------
                                                                           input.ds=input.ds, 
                                                                           input.cls=input.cls,
                                                                           gene.ann=gene.ann,
                                                                           gs.db = gs.db,
                                                                           output.directory=output.directory,
                                                                           gs.ann=gs.ann,
                                                                           doc.string=doc.string,
                                                                           non.interactive.run=non.interactive.run,
                                                                           reshuffling.type=reshuffling.type,
                                                                           nperm=nperm,
                                                                           weighted.score.type=weighted.score.type,
                                                                           nom.p.val.threshold=nom.p.val.threshold,
                                                                           fwer.p.val.threshold=fwer.p.val.threshold,
                                                                           fdr.q.val.threshold=fdr.q.val.threshold,
                                                                           topgs=topgs,
                                                                           adjust.FDR.q.val=adjust.FDR.q.val,
                                                                           gs.size.threshold.min=gs.size.threshold.min,
                                                                           gs.size.threshold.max=gs.size.threshold.max,
                                                                           reverse.sign=reverse.sign,
                                                                           preproc.type=preproc.type,
                                                                           random.seed=random.seed,
                                                                           perm.type=perm.type,
                                                                           fraction=fraction,
                                                                           replace=replace,
                                                                           save.intermediate.results=save.intermediate.results,
                                                                           OLD.GSEA=OLD.GSEA,
                                                                           use.fast.enrichment.routine=use.fast.enrichment.routine
  )
  
}