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Support Assay5 assays stored in seurat objects #22

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esiegel opened this issue Dec 1, 2023 · 0 comments · Fixed by #23
Closed

Support Assay5 assays stored in seurat objects #22

esiegel opened this issue Dec 1, 2023 · 0 comments · Fixed by #23
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esiegel commented Dec 1, 2023

This fails with a missing counts matrix when the assay is of type SeuratObject::Assay5 instead of SeuratObject::Assay

assay <- seurat_obj[["RNA"]]
counts <- assay@counts

For Assay5 it seems we need to grab the data from the layers slot

assay <- seurat_obj[["RNA"]]
counts <- assay@layers[["counts"]]
@esiegel esiegel self-assigned this Dec 1, 2023
@esiegel esiegel added the bug Something isn't working label Dec 1, 2023
@esiegel esiegel mentioned this issue Dec 3, 2023
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Add support for assays stored as SeuratObject::Assay5 10XGenomics/loupeR
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