R/test.correlation.R

In RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

test.correlation<-function (x, param, method.cor = "kendall", method.padj = "BH", file = "correlation_plot.pdf") 
{
  data <- select.measurements(x)
  pvals <- c(NULL)
  tauvals <- c(NULL)
  for (k in 1:ncol(data[[1]])) {
    rval <- cor.test(data[[1]][, k], data[[4]][, param], method = method.cor)
    pvals <- c(pvals, rval[[3]][1])
    tauvals <- c(tauvals, rval[[4]][1])
  }
  adjustedp <- p.adjust(pvals, method = method.padj)
  count <- 0
  pdf(file = file)
  for (k in 1:ncol(data[[1]])) {
    count <- count + 1
    par(lwd = 2)
    plot(data[[1]][, k], data[[4]][, param], xlab = paste(data[[3]]["target", k], "expression"), ylab = param, 
         main = c(paste("correlation of", data[[3]]["target", k], "expression"), paste("to", param), 
                  paste("correlation:  ", round(tauvals[count], digits = 3), "  ", "p-value:  ", 
                  signif(adjustedp[count], digits = 4))), pch = 2, col = "red")
    elem<-lm(data[[4]][, param] ~ data[[1]][, k])
    if(!any(is.na(elem$coefficients))){
      abline(elem, col = "darkgreen")
    }
  }
  dev.off()
}