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quadbio / Pando

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

Seurat object format issues #8

Closed komalbollepogu closed 2 years ago

komalbollepogu commented 2 years ago

Hello, thank you for the wonderful tool. I am getting this error when I try to initiate_grn function: Error in UseMethod(generic = "Annotation", object = object) : no applicable method for 'Annotation' applied to an object of class "Assay". Can you please let me know where I am doing this wrong? I integrated my scATAC and scRNA seq and used the coembeded file as the input file. Does this work? Thanks again!

joschif commented 2 years ago

Hey @komalbollepogu, can you check if the assay in the seurat object that holds your ATAC-seq data is a ChromatinAssay? seurat has a special class for it and it should also have a gene annotation defined that you can access with Annotation().

komalbollepogu commented 2 years ago

Hello, thank you for the quick reply. I just checked and realized that the chromatin assay is missing in the RNA and ATAC integrated object. I will add the chromatin assay and try it again. Thanks so much!

joschif commented 2 years ago

I'll close this since it seems to be resolved. Just let me know if any issues remain. Cheers, Jonas