[Bioc-devel] set.seed and BiocParallel

Bemis, Kylie k@bem|@ @end|ng |rom northe@@tern@edu
Tue Mar 12 22:20:05 CET 2019

Hi all,

I remember similar questions coming up before, but couldn’t track any down that directly pertain to my situation.

Suppose I want to use bplapply() in a function to fit models to many features, and I am applying over features. The models are stochastic, and I want the results to be reproducible, and preferably use the same RNG seed for each feature. So I could do:

fitModels <- function(object, seed=1, BPPARAM=bpparam()) {
bplapply(object, function(x) {

But the BioC guidelines say not to use set.seed() inside function code, and I’ve seen other questions answered saying not to use “seed” as a function parameter in this way.

Is it preferable to check and modify .Random.seed directly, or is there some other standard way of doing this?


Kylie Ariel Bemis
Khoury College of Computer Sciences
Northeastern University

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