partial correlation and conditions

Question

[moxu]

I have RNA-seq (and thus gene counts) samples from cell type 1, and samples from cell type2. Each sample had been treated with control and a compound of varying concentrations. "ridge.net" of R package "parcor" is used to derive the partial correlation matrix: construct a gene count matrix "d" with each column being a gene and each row being a sample, and use "ridge.net(d, k=10)" to get the parcor matrix.

Question: the compound concentration and cell type information seems to be wasted. Is there a way to incorporate such info into partial correlation computation?

Thanks in advance!