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TaoYang-dev / hicrep

R package to evaluate the reproducibility of Hi-C data
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Could the fast.mean.filter be used in the analysis? #59

Open liufuyan2016 opened 6 years ago

liufuyan2016 commented 6 years ago

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 commented 6 years ago

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.