Contact number decreases after merging replicates?

[hackkr]

Hello,

I was wondering if you could provide more detail about the merge() function. When I merge biological replicates, I often see a decrease in the number of contacts in the merged HiCExperiment object. Is this due to renormalization after merging?

In future updates, it would be nice to see the merge reflected in the object metadata (e.g. FileName and pairsFile)!

biorep1:

`HiCExperiment` object with 7,919,014 contacts over 2,466 regions 
-------
fileName: "hicstuff_trimmed/T0_minus_A.mcool" 
active resolution: 1000 
interactions: 2687955 
scores(2): count balanced 
topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) 
pairsFile: hicstuff_trimmed/T0_minus_A.valid_idx_pcrfree.pairs.gz 
metadata(0):

biorep 2:

`HiCExperiment` object with 2,200,083 contacts over 2,466 regions 
-------
fileName: "hicstuff_trimmed/T0_minus_B.mcool" 
active resolution: 1000 
interactions: 1433302 
scores(2): count balanced 
topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) 
pairsFile: hicstuff_trimmed/T0_minus_B.valid_idx_pcrfree.pairs.gz 
metadata(0):

merged:

`HiCExperiment` object with 7,071,843 contacts over 2,466 regions 
-------
fileName: "hicstuff_trimmed/T0_minus_A.mcool" 
active resolution: 1000 
interactions: 2822791 
scores(2): count balanced 
topologicalFeatures: () 
pairsFile: N/A 
metadata(2): hce_list operation