Could the fast.mean.filter be used in the analysis?

[liufuyan2016]

I read the manual carefully, and I want to make the following steps is right? Thank you!

h_hat <- htrain(HiCR1, HiCR2, 1000000, lbr = 0, ubr = 5000000, range = 0:2)
smd_mat1 = fast.mean.filter(HiCR1, 2)
smd_mat2 = fast.mean.filter(HiCR2, 2)
scc.out = get.scc(smd_mat1, smd_mat2, 1000000, 2, 0, 5000000)

[TaoYang-dev]

I don't see a problem here. One thing I would like to comment here is that, when you train the smoothing parameter, make sure you use a sufficiently sequenced Hi-C data. When the sequencing depth is low, the training process could give you inflated smoothing parameter. You might also want to make your range bigger just to expand the searching scope.