Difference between input matrix value and GENOVA matrix object

[Lucas446]

Hi,

I have a question concerning the import of .cool HiC matrix (From HiCexplorer ConvertFormat .h5 to .cool, the .h5 has been normalized using KR).

I realized that the load_contacts function of GENOVA is applying a factor (independent of the balancing option) to the data when comparing the values in $MAT$V4 and the value from the input,

Do you know where is this factor is coming from ?

Thanks a lot, Best, Tanguy

[robinweide]

Dear Tanguy,

This is a depth-normalization and can be stopped by setting scale_bp = NULL.

Best, Robin

[Lucas446]

Perfect, it works great!