[R] speeding up 1000s of coxph regression?

[Xiao-Jun Ma]

I have a gene expression matrix n (genes) X p (cases), where n = 8000 and p
= 100. I want to fit each gene as univariate in a coxph model, i.e., fitting
8000 models. I do something like this:

res <- apply(data, 1, coxph.func)

which takes about 4 min, not bad. But I need to do large numbers of
permutations of the data (permuting the columns), for example, 2000, which
would take 5 days. I would like to know if there is way to speed this up?

Any help appreciated.

Xiao-Jun