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quadbio / Pando

Multiome GRN inference.
https://quadbio.github.io/Pando/
MIT License
106 stars 21 forks source link

Feature selection #9

Closed zhenzuo2 closed 1 year ago

zhenzuo2 commented 1 year ago

Hi,

Is FindVariableFeatures() needed before running pando? I am not sure which assay or matrix pando used for RNA seq data. Thank you.

joschif commented 1 year ago

Hi @zhenzuo2, if you run FindVariableFeatures() before running Pando, the default behavior is to only consider the selected features for GRN inference. However, you can directly choose the set of genes through the argument genes in infer_grn(). Also, you can set the assays to be used with the peak_assay and rna_assay arguments to initiate_grn(). Within these assays Pando will always use the normalized data slot. I hope this helps, cheers!

joschif commented 1 year ago

I'll close this now, but feel free to reopen if you have further questions