Edger - Run Glm On Only One Gene

Question

[bbio]

I would like to use edgeR's GLM functionality to determine the influence of several factors on a gene's expression levels. For performance reasons I would like to estimate the dispersion using the entire count table, but then determine the fit just for the gene I am interested in.

Is there any way to do this, i.e. call glmFit() on just one row of the table? I already tried to create a new CDS for just the gene and copy over the dispersion from the full CDS, but that does not seem to work.

Answer 1

[Steve Lianoglou]

It does fit the glm one gene/transcript/unit/whatever at a time. I'm curious what you want to do with it?

Anyway, you can get the params of the fit from the result of your call to glmFit(...), no? Look at all the stuff you get back in the "Value" section of ?edgeR::glmFit

[bbio]

I know that it does the fit one gene at a time, but I only want to obtain the fit for one specific gene anyway. So it would be quite a waste of computing time if I did the fit for every single gene, just to ignore everything but one line afterwards. I was hoping there was some way to use the entire count table for dispersion estimation, but then only do the fitting on the relevant row.