R/Signif.R

In IsoGeneGUI: A graphical user interface to conduct a dose-response analysis of microarray data

`Signif` <-
function (rpval, FDR, type = c("BH", "BY","Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD"))
  {
    adjp <- adjustment(rpval, type)
    sig  <- which(adjp[, 2] <= FDR)
    if (length(sig) == 0 ) {
                   print("no gene is significant")
                   }
    else {
          if (length(sig) > 1) {
              adjp1 <- data.frame(sig, adjp[sig,])
               }
          else  {
               adjp1 <- c(sig, adjp[sig,])
	         }
          names(adjp1) <- c("row.num", "raw p-values", paste (type, sep = " ", "p-values"))
          return(adjp1)
	    }

    }