Concern related to function "intra_inter_TAD"

[ccmeth]

Hi, developers,

Thanks a lot for providing such a powerful tool for us to analyze Hi-C data, recently I used results obtained from "intra_inter_TAD" to compare the TAD insulation variation between different samples. I wondered whether elements in Hi-C main diagonal were considered when calculating intra-TAD interactions?

Thanks again, Hao

[teunbrand]

Hi there,

Yes the main diagonal would be included in these calculations. If you want to exclude this, you can load the data with load_contacts(..., z_norm = TRUE).

[ccmeth]

Hi there,

Yes the main diagonal would be included in these calculations. If you want to exclude this, you can load the data with load_contacts(..., z_norm = TRUE).

Thanks for your reply! Another issue I wondered is the parameter used to evaluate the TAD insulation variation. I have seen various parameters in different papers such as the ration between inter-TAD and intra-TAD interactions, inter-TAD interactions, and insulation score calculated by GENOVA. Which one was more proper?

[ccmeth]

Sorry, I still have another question related to Figure 4c of your paper published in NAR Genomics and Bioinformatics, how can I draw the concrete numbers indicating the A-A, B-B and A-B interactions? Function "visualise" did not show them.