How to add CARD result to Seurat object

[GouQiao]

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]

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]

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