Hi- I have some RNA-seq data from a series of 4 isogenic strains (0,1,2,3), differing in their copy number of a single gene. I would now like to identify those genes whose expression changes across these samples in proportion to the copy number of the gene of interest.
For e.g., in the series 0,1,2,3, what genes show proportional increase in tpm/fpkm as we go from 0 to 3, and what genes show proportional decrease.
I imagine I should be able to model this in DESeq2, but am unable to exactly figure out how. Any pointers/help will be appreciated. Open to using methods other than DESeq2 too, if needed.
Thanks in advance.