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YMa-lab / CARD

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How to add CARD result to Seurat object #75

Open GouQiao opened 2 months ago

GouQiao commented 2 months ago

Hi developer,

Thanks for developing such amazing package for ST analysis. After deconvolution by CARD, how to add the results of CARD object to Seurat data for downstream analysis ? for example, add the info into meta.data of Seurat object.

best,

YMalab commented 2 months ago

Hi @GouQiao,

Thank you for the question!

I think you can add the cell type compositions from CARD into Seurat by manually adding it to:

seuratObject[["predictions"]] <- predictions.assay #### this could be the place you put the cell type compositions
DefaultAssay(slide.seq) <- "predictions"

Please see more details in their tutorial: https://satijalab.org/seurat/articles/spatial_vignette

We can work on that later since it takes some time for us to check the details.

Best, Ying

GouQiao commented 2 months ago

Thanks for your patient reply. Which data from the CARD object should be extracted to make the matrix of predictions.assay?