Unable to find 'nCount_peaks' in Signac data

stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data

https://stuartlab.org/signac/

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Unable to find 'nCount_peaks' in Signac data #1772

Closed ptk1601 closed 2 months ago

ptk1601 commented 2 months ago

Hello!

Major thanks for making such an amazing R package. I am trying to find significant motifs in my Signac data. Unfortunately, I cannot find the 'nCount_peaks' variable in my data to generate the da_peaks object. Rather, all I see is nCount_RNA and nCount_ATAC. Is there something I missed while integrating my multiome data? Would love to see if I can find any solutions!

timoast commented 2 months ago

Hi, can you show the code you're running?

timoast commented 2 months ago

it looks like you named your assay "ATAC" rather than "peaks"

the nCount information is added for each assay, and named according to the assay name. In your case the information will be stored as nCount_ATAC