When using the Quasi-Likelihood dispersions via glmQLFit in
edgeR, and providing a
DGEList as input, the function
glmQLFit.DGEList() explicitly passes the value
lib.size = NULL to the lower-level function
glmQLFit(). This forces the library sizes to be the column sums when passed eventually to the lower-level function
.compressOffsets(). I'm really struggling to see the justification for this.
My situation is that I'm using sliding windows via the workflow presented at https://f1000research.com/articles/4-1080/v2 and as such, the library size is not the sum of the reads in each column. I would like to use the correct library sizes I have assigned to the
lib.size element of my
DGEList. Clearly, I can just write my own function to get around this. However, is this an intentional decision with solid reasoning that's beyond me, or just one that slipped through?
Thanks Andy. That makes sense for sure.
The precedence of offset over lib.size is documented on the glmQLFit help page.