In my implementation of the DESeq2 Rmd steps, I've separated things out by comparison. This means that each comparison exports counts & vst matrices for the samples w/in this comparison; however, there is no global matrix exported with all samples. To implement this, two options come to mind:
- this could be it's own short independent rule, or
- we could rework the entire DESeq2 rule to go back to a one-Rmd approach (just lapplying through each comparison, as Kin originally had it, iirc)
Creating this issue so we implement this eventually, regardless of which route we choose.
In my implementation of the DESeq2 Rmd steps, I've separated things out by comparison. This means that each comparison exports counts & vst matrices for the samples w/in this comparison; however, there is no global matrix exported with all samples. To implement this, two options come to mind:
Creating this issue so we implement this eventually, regardless of which route we choose.