statOmics/tradeSeq

Remove spurious rowData calls in hypothesis tests.

jgilis opened this issue · 1 comments

jgilis commented

At the moment, the different hypothesis tests run slower on GAM object than on SCE objects.
This is because of spurious rowData calls, which are required for obtaining the betas and sigmas, inside a lapply loop.
For example in diffEndtest:

tradeSeq/R/diffEndTest.R

Line 87 in 84ab467

beta <- t(rowData(models)$tradeSeq$beta[[1]][ii,])

Suggested enhancement: move the rowData call upstream of the loop and call only once.

koenvandenberge commented

This has now been adapted, thanks!

  • 👍1