Find interaction regions from HiC contact matrix?

Question

[star]

I downloaded a HiC normalized contact matrix like below (a subset of dig table). it is based on a 10kb resolution. The rows and columns should be the genomic coordinates based on 10000bp interval (e.g: Chr 18 length is 78,022,248 bp and the dimension of Chr 18 contact matrix is 7803*7803).

df_subset

           V1       V2        V3         V4       V5        V6     
1    0.000000    0.000   0.00000   93.25807 0.000000 823.45363 
2    0.000000    0.000   0.00000 1063.53307 0.000000   0.00000
3    0.000000    0.000   0.00000    0.00000 0.000000 415.63635 
4   93.258072 1063.533   0.00000    0.00000 0.000000  68.68992 
5   0.000000     0.000   0.00000    0.00000 0.000000   0.00000 
6  823.453631    0.000 415.63635   68.68992 0.000000   0.00000

I am a bit confused, it is the first time that I would like to work with HiC data. So I would like to find the interaction between locations and I faced with some questions:

• how can I consider the genomic locations (based on 10 kb resolution), Cal I use seq (start, end,by=10000) function afterward put it as colnames and rownames?
• How can I understand which interactions are significant?
• is the coordinate in contact matrix sorted?

Many thanks in advance!

[Kay]

Hi Star, I now came across the same "significant contact calling" problem as you, so I wonder whether you found the answer already? Many thanks!