cellcall with integrated data (Seurat)

[akramdi]

Hello,

Could you give us some indications on how to create the right input data for cellcall in case of integrated data (Seurat)? We plan to extract expression data from the "counts" slots of the "SCT" assay, does this sound reasonable ?

Many thanks fot the help,

[ShellyCoder]

Apologize for a late reply. If you want to extract count data of endothelial_cell from the seurat object "seurat_obj". The example code has followed:

yourDF <- as.matrix(GetAssayData(seurat_obj, slot = "counts")[, WhichCells(seurat_obj, ident = "endothelial_cell")])