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Toy Seurat object for examples and tests

toy_seurat.Rd

Builds a small deterministic Seurat object (20 genes x 300 cells, two cell types in the cell_type metadata column) with the installed Seurat version, so no serialized object needs to ship with the package or be updated when Seurat changes its internal class structure. Counts are Poisson-simulated with a few upregulated marker genes per cell type, and log-normalized into the data layer. The generator restores the caller's random-number state, so calling it does not perturb reproducibility.

Usage

toy_seurat()

Value

A Seurat object with counts and data layers and a cell_type metadata column with values "jurkat" and "t293".

Details

Requires the suggested package Seurat.

See also

toy_sce(), wilcoxauc()

Examples

if (requireNamespace("Seurat", quietly = TRUE)) {
    object_seurat <- toy_seurat()
    head(wilcoxauc(object_seurat, "cell_type"))
}
#>   feature  group  avgExpr     logFC statistic        auc         pval
#> 1      G1 jurkat 7.044320  2.402634   22061.0 0.98048889 4.798334e-47
#> 2      G2 jurkat 7.023134  2.436198   22127.0 0.98342222 1.345320e-47
#> 3      G3 jurkat 7.057136  2.092308   21980.0 0.97688889 2.524538e-46
#> 4      G4 jurkat 3.968689 -3.058986     411.0 0.01826667 1.851896e-47
#> 5      G5 jurkat 4.521172 -2.516202     496.0 0.02204444 1.392045e-46
#> 6      G6 jurkat 4.497776 -2.538578     566.5 0.02517778 5.193532e-46
#>           padj    pct_in   pct_out
#> 1 3.198889e-46 100.00000  75.33333
#> 2 1.851896e-46 100.00000  75.33333
#> 3 1.009815e-45 100.00000  80.66667
#> 4 1.851896e-46  64.00000 100.00000
#> 5 6.960227e-46  74.00000 100.00000
#> 6 1.731177e-45  72.66667 100.00000