R/globalFisher.R

In globalGSA: Global Gene-Set Analysis for Association Studies.

globalFisher <-
function(data, B, gene_list, Gene="all", addit=FALSE, covariable=NULL, family=binomial) {
  Geno <- data[,-1]
  Trait <- factor(data[,1])
  output <- NULL
  output$nPerm <- B
  if(Gene!="all") {
    data <- data.frame(Trait, Selected_genes(Gene, gene_list, data))
    output$Gene <- Gene  
  }
  x <- GeneratePvalues(data, B, addit, covariable, family)
  output$genevalue <- 1-pchisq(-2 * sum(log(x)),df=2*length(x))
  return(output)
}