Example single-cell RNA-seq data (multi–cell type)

A small SingleCellExperiment object used as example input for scDesignPop functions. It contains a subset of genes and cells from the OneK1K cohort with associated individual and cell-type metadata.

A subset of the scRNA-seq data from the OneK1K cohort which has been anonymized.

Usage

data("example_sce")

data("example_sce")

Format

A SingleCellExperiment object with 1,000 genes and 7,811 cells.

assays

• counts: raw UMI count matrix (genes x cells).

• logcounts: log-normalized expression values.

rowData

(empty in this toy example).

colData

A DataFrame with 4 columns:

indiv

Individual identifier (e.g., "SAMP1", "SAMP2").

cell_type

Cell-type annotation (e.g., T cells, B cells, NK cells).

sex

Sex of the donor.

age

Age of the donor.

reducedDimNames

None in this example.

example_sce

A data frame with 100 genes (rows) and 17,918 cells (cols) for 20 individuals :

cell_type

Cell type

indiv

Individual id

Examples

data("example_sce")
example_sce
#> class: SingleCellExperiment 
#> dim: 1000 7811 
#> metadata(0):
#> assays(2): counts logcounts
#> rownames(1000): ENSG00000023902 ENSG00000027869 ... ENSG00000254709
#>   ENSG00000272216
#> rowData names(0):
#> colnames: NULL
#> colData names(5): indiv cell_type sex age batch
#> reducedDimNames(0):
#> mainExpName: RNA
#> altExpNames(0):
table(SingleCellExperiment::colData(example_sce)$cell_type)
#> 
#>  monoc mononc   bmem  cd4nc 
#>   1750    689   1766   3606