Function to access object data

Usage

object_data(object, ...)

# S3 method for Seurat
object_data(object, slot, n_genes = 1000, ...)

# S3 method for SingleCellExperiment
object_data(object, slot, ...)

Arguments

object: object after tsne or umap projections and clustering
...: additional arguments
slot: data to access
n_genes: number of genes limit for Seurat variable genes, by default 1000, set to 0 to use all variable genes (generally not recommended)

Value

expression matrix, with genes as row names, and cell types as column names

Examples

so <- so_pbmc()
mat <- object_data(
    object = so,
    slot = "data"
)
mat[1:3, 1:3]
#> 3 x 3 sparse Matrix of class "dgCMatrix"
#>        AAACATACAACCAC AAACATTGAGCTAC AAACATTGATCAGC
#> PPBP         .              .              .       
#> LYZ          1.635873       1.962726       1.995416
#> S100A9       .              .              .       
sce <- sce_pbmc()
mat <- object_data(
    object = sce,
    slot = "data"
)
mat[1:3, 1:3]
#> 3 x 3 sparse Matrix of class "dgCMatrix"
#>        AAACATACAACCAC AAACATTGAGCTAC AAACATTGATCAGC
#> PPBP         .              .              .       
#> LYZ          1.635873       1.962726       1.995416
#> S100A9       .              .              .