R/featureselection.R

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

featureselection <-
function (gnExpMat, survivaltime, censor, method = "none",gn.nb){
        ploglik = NULL
        cox.coef = NULL

        max.col = ifelse (is.matrix(gnExpMat), ncol(gnExpMat), 1)

        for (i in 1:max.col){
                if(is.matrix(gnExpMat))
                        var = gnExpMat[,i]
                else
                        var = gnExpMat
                cox.t = coxph(Surv (survivaltime, censor)~var)          
                ltest <- -2 * (cox.t$loglik[1] - cox.t$loglik[2])
                pv <- 1 - pchisq(ltest, 1)
                ploglik = c (ploglik, pv)
                cox.coef = c(cox.coef, cox.t$coef)
        }
	ploglik <- p.adjust(ploglik,method=method)

	if (method == "none")
		ploglik = order(ploglik)[1:gn.nb]
	else{
		ploglik = (ploglik<= .05)	
		gn.nb = sum(ploglik)
		cat ("Selected genes nb: ", gn.nb, "\n")
	}
  return (ploglik)
}