R/absoluteTest.genePvalsFAST.R

In arcolombo/junk: qusage: Quantitative Set Analysis for Gene Expression

#' function to calculate the homogeneity P value faster
#' @param QSarray A QSarray object, as generated by aggregateGeneSet and possibly modified by calcVIF
#' @param CompareWithZero Logical, if TRUE compares with mean of zero, else with mean of pathway
#' @export
#' @return p values faster
absoluteTest.genePvalsFAST<-function(QSarray,  ##A QSarray object, as generated by aggregateGeneSet and possibly modified by calcVIF
                              CompareWithZero=TRUE ###Logical, if TRUE compares with mean of zero, else with mean of pathway
){
  if(is.null(QSarray$pathways)){stop("Pathway Information not found. Please provide a list of gene sets.")}
  geneSets = QSarray$pathways
  Means = QSarray$mean
  SD = QSarray$SD
  DOF=QSarray$dof
  Ps = list()
  for(i in 1:length(geneSets)){
    Indexes = geneSets[[i]]
    if(length(Indexes)!=0){
      PS<-NULL

      PS<-sapply(Indexes,function(j){
        SUBSTRACT=0
        if(!CompareWithZero)SUBSTRACT=QSarray$path.mean[i]
        p<-pt((Means[j]-SUBSTRACT)/SD[j],DOF[j])
        p[which(p>0.5)] = -1+p[which(p>0.5)]   ### turn it into a two-tailed p
        p = p*2
        return(p)
      })
      Ps[[i]]<-PS
    }
  }
  names(Ps) = names(geneSets)
  return(Ps)
}