R/coxstuff.R

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

##### internal functions from Dr. Tibshirani's software package GSA
coxstuff <-
function(x, y, ic, offset = rep(0., length(y)))
{
        fail.times <- unique(y[ic == 1.])
        nf <- length(fail.times)
        n <- length(y)
        nn <- rep(0., nf)
        nno <- rep(0., nf)
        for(i in 1.:nf) {
                nn[i] <- sum(y >= fail.times[i])
                nno[i] <- sum(exp(offset)[y >= fail.times[i]])
        }
        s <- matrix(0., ncol = nf, nrow = nrow(x))
        d <- rep(0., nf)
        #expand d out to a vector of length n
        for(i in 1.:nf) {
                o <- (1.:n)[(y == fail.times[i]) & (ic == 1.)]
                d[i] <- length(o)
}
         oo <- match(y, fail.times)
         oo[ic==0]<-NA
         oo[is.na(oo)]<- max(oo[!is.na(oo)])+1
         s<-t(rowsum(t(x),oo))
       if(ncol(s)> nf){s<-s[,-ncol(s)]}
        dd <- rep(0., n)
        for(j in 1.:nf) {
                dd[(y == fail.times[j]) & (ic == 1.)] <- d[j]
        }
        return(list(fail.times=fail.times, s=s, d=d, dd=dd, nf=nf, nn=nn, nno=nno))
}