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quadbio / Pando

Multiome GRN inference.
https://quadbio.github.io/Pando/
MIT License
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cannot find some regions meta.features #6

Closed zhenzuo2 closed 2 years ago

zhenzuo2 commented 2 years ago

Hi,

I found some regions identified at modules@meta are not among seurat_object@assays$peaks@meta.features.

For example, it is chr15-89214422-89215304 in modules@meta but chr15-89214422-89215059 in seurat_object meta.features.

Thank you!

joschif commented 2 years ago

Hi @zhenzuo2, depending on how you are selecting candidate regions, the regions used by Pando don't directly correspond to peaks. Have you used the regions argument in initiate_grn()? If so, the regions in Pando are an intersection of the peaks and those provided regions.

joschif commented 2 years ago

I'm closing this since there has not been any activity. Feel free to reopen it if the issue persists.

zhenzuo2 commented 2 years ago

Thank you for your reply @joschif ! I found a few interesting TF-gene pairs and I want to plot peak counts for the candidate regions, gene expression, and TF expression. Is there any way I can extract those numbers from the fitted seurat_obejct? Thank you.