R/coxscor.R

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

##### internal functions from Dr. Tibshirani's software package GSA
coxscor <-
function(x, y, ic, offset = rep(0., length(y)))
{
        # computes cox scor function for rows of nx by n matrix  x
 # first put everything in time order
        n <- length(y)
        nx <- nrow(x)
        yy <- y + (ic == 0.) * (1e-05)
        otag <- order(yy)
        y <- y[otag]
        ic <- ic[otag]
        x <- x[, otag, drop = F]
        #compute  unique failure times, d=# of deaths at each failure time, 
        #dd= expanded version of d to length n, s=sum of covariates at each
        # failure time, nn=#obs in each risk set, nno=sum(exp(offset)) at each failure time
        offset <- offset[otag]
        a <- coxstuff(x, y, ic, offset = offset)
        nf <- a$nf
        fail.times <- a$fail.times
        s <- a$s
        d <- a$d
        dd <- a$dd
        nn <- a$nn
        nno <- a$nno
        w <- rep(0., nx)
        for(i in (1.:nf)) {
                w <- w + s[, i]
                oo<- (1.:n)[y >= fail.times[i]]
                r<-rowSums(x[, oo, drop = F] * exp(offset[oo]))
                w<- w - (d[i]/nno[i])*r 
        }
        return(list(scor = w, coxstuff.obj = a))
}