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Personalized RIV and region_to_gene tables #9
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Hi Rémi, Thanks for these good questions!
Yes, they are both generated randomly and independently. RIV is sampled from a distribution controlled by
If you need to encode information about the regions, these matrices are definitely the right place to put it. We simplified the ATAC part because there was too much other work in this project, and we plan to improve this in the future. However, although this works theoretically, you may need to do some tests to see how well this information is encoded in the simulated data.
Yes, I think continuous values will also work, because basically
I may need some time to update the package and make it a general option. In the mean time, you may modify the code directly. You can find calls to these functions in
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Thanks a lot for this detailed answer ! I will try to modify these 2 functions and if this specific case interests you too, I'll let you know how the simulation results look like :) |
Hi dear developers!
Thanks a lot for this very interesting tool :)
It works very fast and intuitively !
I would like to use scMultiSim data in the context of a GRN inference method from multi-omics data, and in this context I had some questions about ATAC influence on gene expression and how I could personalize region-to-gene table.
I'm interested in a setup where the CIF-gene links are only based on the combination of CIF-ATAC and ATAC-genes, to explore how methods can make use of TF-regions/regions-genes informations to retrieve the corresponding GRN.
Thanks a lot for your feedbacks!!
Rémi
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