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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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how to define signicantly differential compartment switch #6

Closed BenxiaHu closed 3 years ago

BenxiaHu commented 3 years ago

Hi, when I checked out the _differentialcompartments.bedGraph file generated by dcHiC, the number of differential compartments is about 100. However, when I extracted significantly differential compartments at the FDR of 0.05 0r 0.01, from _full_compartment_details.bedGraph_, the number of significantly differential compartments is greater than 1000.

Could you explain to me how dcHiC output the _differentialcompartments.bedGraph file?

Another question: How to define High B and low B? for example, the PC scores in a given region between 2 different conditions (tumor and normal) are -4 and -1, respectively. So the tumor in this region is defined as High B or Low B?

Best,

ay-lab commented 3 years ago

Hello,

Apologies about the delayed reply. "High B" is defined as a strong B compartment (-4) and "low B" is defined as a weak B compartment (-1). If your tumor is -4, it has stronger B compartmentalization ("high B) compared to your normal cell line.

With regard to the differential calling—thank you for pointing out the discrepancy. It seems that a small deprecated feature wasn't properly updated; the numbers should now match if you use the latest "diffcmp_pythonV.R" file in the GitHub.