search

ma-compbio / Fast-Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition
MIT License
17 stars 5 forks source link

Need the imputed scHi-C matrices #8

Open gmurtaza404 opened 6 months ago

gmurtaza404 commented 6 months ago

Hello! Thank you for sharing your code with us and the very detailed Wiki to walk us through the setup process.

I wanted to ask, how do I acquire the imputed matrices from the Fast-Higashi? I know you run a partial_rwr algorithm to generate imputed scHi-C matrices. Is this function adaptable to any tensor of scHi-C matrices? Does the input "x" to this function require the tensor to be arranged in a certain way, for example the scHi-C matrices of the same cell type are closer to each other in the tensor (think of axis 0)? Or can I just borrow this function and run it on my own scHi-C data tensors without any order?

Thanks again!

ruochiz commented 6 months ago

Hah, we actually have that created (but it's a rare use cases, so was excluded):

model.prep_dataset()
model.only_partial_rwr()

It has been a while since I use that function, but lmk if you run into any errors

gmurtaza404 commented 6 months ago

Thanks! Ill get back to you on this after I have tried it out! But usually if the data is good, we should not need any imputations right?