R/splitZscore2.auc.plot.R

In survJamda: Survival Prediction by Joint Analysis of Microarray Gene Expression Data

splitZscore2.auc.plot <-
function (common.gene, geno.files, surv.data,lst, i,j, col,method, time.dep)
{
	train.ind = NULL

	cat ("Normalization = Zscore2\n")
	
	cat ("Train data sets: ")
	for (m in i)
		cat (geno.files[m], " ")
	train.ind = 1:nrow(lst$mat)

	test.phyno = comb.surv.censor(geno.files,c(j),surv.data)

	test = get(geno.files[j])[!is.na(test.phyno$surv),common.gene]
	test = scale(t(scale(t(test))))

	lst$mat = rbind (lst$mat, test)

	test.phyno$censor = test.phyno$censor[!is.na(test.phyno$surv)]
	test.phyno$surv = test.phyno$surv[!is.na(test.phyno$surv)]

	lst$phyno$surv = c(lst$phyno$surv, test.phyno$surv)
	lst$phyno$censor = c(lst$phyno$censor, test.phyno$censor)

	cat("Test data set: ", geno.files[j], "\n")

	test.ind = (length(train.ind)+1):nrow(lst$mat)

	calPerformance.auc.plot(lst, train.ind, test.ind, geno.files[j],col,method, "Zscore2", time.dep)
}