Inspects the structure and contents of a supported single-cell data file without performing a conversion. Supported inputs include Seurat and SingleCellExperiment objects stored as RDS files, AnnData H5AD files, and Loom files.
Value
Invisibly returns a list containing information about the inspected object. The contents of the list depend on the input format.
Details
The function reports basic information such as the number of cells and features, available assays or layers, dimensional reductions, metadata, and a sample of cell names. Additional format-specific information is reported when available.
Examples
if (requireNamespace("Seurat", quietly = TRUE)) {
counts <- matrix(
c(1, 0, 3, 0, 2, 1),
nrow = 2,
dimnames = list(
c("Gene1", "Gene2"),
c("Cell1", "Cell2", "Cell3")
)
)
obj <- Seurat::CreateSeuratObject(counts = counts)
path <- tempfile(fileext = ".rds")
saveRDS(obj, path)
inspect_sc(path)
unlink(path)
}
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
#> RDS file detected.
#> Seurat object detected.
#> Version of Seurat: 5.4.0
#> Number of cells: 3
#> Number of features: 2
#> Assays [1]: RNA
#> Default assay: RNA
#> Default assay structure: Assay5
#> Default assay layers [1]: counts
#> Reductions [0]: None
#> Graphs [0]: None
#> Neighbors [0]: None
#> Metadata columns [3]: orig.ident, nCount_RNA, nFeature_RNA
#> Sample of cell names: Cell1, Cell3, Cell2