R/coxvar.R

In MetaPath: Perform the Meta-Analysis for Pathway Enrichment Analysis (MAPE)

##### internal functions from Dr. Tibshirani's software package GSA
coxvar <-
function(x, y, ic, offset = rep(0., length(y)), coxstuff.obj = NULL) {
        # computes information elements (var) for cox
        # x is nx by n matrix of expression  values
        nx <- nrow(x)
        n <- length(y)
        yy <- y + (ic == 0.) * (1e-06)
        otag <- order(yy)
        y <- y[otag]
        ic <- ic[otag]
        x <- x[, otag, drop = F]
        offset <- offset[otag]
        if(is.null(coxstuff.obj)) {
                coxstuff.obj <- coxstuff(x, y, ic, offset = offset)
        }
        nf <- coxstuff.obj$nf
        fail.times <- coxstuff.obj$fail.times
        s <- coxstuff.obj$s
        d <- coxstuff.obj$d
        dd <- coxstuff.obj$dd
        nn <- coxstuff.obj$nn
        nno <- coxstuff.obj$nno

	x2<- x^2
	oo <- (1.:n)[y >= fail.times[1] ]
	sx<-(1/nno[1])*rowSums(x[, oo] * exp(offset[oo]))
	s<-(1/nno[1])*rowSums(x2[, oo] * exp(offset[oo]))
	w <-  d[1] * (s - sx * sx)

       for(i in 2.:nf) {
           oo <- (1.:n)[y >= fail.times[i-1] & y < fail.times[i] ]
      sx<-(1/nno[i])*(nno[i-1]*sx-rowSums(x[, oo,drop=F] * exp(offset[oo])))
         s<-(1/nno[i])*(nno[i-1]*s-rowSums(x2[, oo,drop=F] * exp(offset[oo])))
       w <- w + d[i] * (s - sx * sx)
        }
        return(w)
}