Gets a data frame from a Seurat object

Provided a Seurat object, returs a data frame of the count values, being the columns each 'gene' and the rows each UMI/cell.

# S3 method for Seurat
as.data.frame(x, genes = Seurat::VariableFeatures(x), fix_names = TRUE, ...)

Arguments

x	A Seurat object
genes	genes to extract to the data.frame
fix_names	logical value indicating wether the gene names should be converted to R-compatible names. defaults to FALSE
...	additional arguments passed to `Seurat::FetchData`

Value

a data frame.

Details

It returns only the genes annotated as variable and the identity column.

Examples

as.data.frame(Seurat::pbmc_small,
    Seurat::VariableFeatures(Seurat::pbmc_small))[1:3,1:3]
#>                    PPBP IGLL5 VDAC3
#> ATGCCAGAACGACT 0.000000     0     0
#> CATGGCCTGTGCAT 0.000000     0     0
#> GAACCTGATGAACC 4.753095     0     0
#                    PPBP IGLL5 VDAC3
# ATGCCAGAACGACT 0.000000     0     0
# CATGGCCTGTGCAT 0.000000     0     0
# GAACCTGATGAACC 4.753095     0     0