Allow missing TFs or missing genes
Currently, the final GRNs after integrating the genes include EITHER TF-peak-gene links (so the peak connections to both TF and gene) OR TF-peak links only, without a peak-gene link. In my current version, I call this somewhat badly "onlyCompleteCases", with "complete" refering to the TF-peak-gene "trio", and if this is set to FALSE, the GRN may also include "non-complete" cases: just TF-peak links without genes.
Is there a need to change this and, for example, also include only peak-gene links, without the TF?
If yes, I have to implement it.