I am performing some differential kinetic analysis on RNA-seq data. I see that the test function adds the groups for which DK is found and a p-value for that (overall p-value? Best/worst p-value across groups?).
Anyhow, I’m more interested in characterizing the deviation from the fitted kinetic for each group, so that I can collect genes with excess of spliced or unspliced species. I’d like to avoid plotting phase diagrams for each significant gene.
I’ve seen that the test builds a model for each gene and one can get group pvalues and mse (which I guess measures the displacement from the system kinetic). Is it possible to derive a signed value that is informative of the excess of (un)spliced transcripts in the phase diagram? Unfortunately most of the code has flags that suggest documentation has not been written yet 