Imagine I have a dataset of highly periodic gene expression, taken at densely spaced timepoints. I know that the expression is periodic, but different genes have different offsets.
It is trivial to convert my timestamps into a cosine (
cos_time = cos(offset + time*pi*2/PERIOD)), so that this new variable is linear with the genes' expressions -- but only with the ones that have a peak at
What if I could have multiple
cos_times (let's call them
phases) and then ask DESeq2: "OK, which gene's behavior is most linear with which phase?" Barring comparing p-values of each LRT test, is there a better way?
Disclaimer: I know about cosinor, Lomb-Scargle periodograms, ARS, JTK etc, and I know they are likely more applicable in this particular case. I'm interested in whether it is in general possible to ask such a question from DESeq2, even if the variables in question are not periodic. Phase just seemed like the simplest concept to demonstrate this on.