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Extract Sample-Level Metadata with Automatic Format Detection

Source: R/preprocess.R
get.meta.Rd

Convenience wrapper that automatically detects input format (Seurat v4/v5, SingleCellExperiment, or HDF5AnnData) and calls the appropriate metadata extraction function. Simplifies workflow by eliminating need to know object version.

Usage

get.meta(.obj, .sample.var, .verbose = TRUE)

Arguments

.obj

Object containing cell-level metadata. Can be:

  • Seurat object (v4 or v5) - calls get.meta.Seurat or get.meta.Seurat5

  • SingleCellExperiment object - calls get.meta.SCE

  • HDF5AnnData object - calls get.meta.HDF5AnnData

.sample.var

Character: column name in object metadata identifying samples.

.verbose

Logical: print progress messages? Default TRUE.

Value

Data frame with one row per sample, containing only sample-level metadata columns. Rownames are sample IDs.

Details

This function inspects the class of .obj to determine format:

  • Seurat: Checks first assay for Assay5 class to distinguish v4 from v5

  • SingleCellExperiment: Uses standard colData accessor

  • HDF5AnnData: Uses obs accessor

Automatically filters to sample-level metadata by testing which columns have consistent values within each sample. Cell-level columns (varying within samples) are excluded with a warning.

See also

get.meta.Seurat, get.meta.Seurat5, get.meta.SCE, get.meta.HDF5AnnData, get.cells for extracting count data

Examples

if (FALSE) { # \dontrun{
# Example 1: Seurat object (auto-detects v4 vs v5)
meta <- get.meta(.obj = seurat.obj,
                 .sample.var = "sample_id")

# Example 2: SingleCellExperiment object
meta <- get.meta(.obj = sce.obj,
                 .sample.var = "Sample")

# Example 3: HDF5AnnData object
meta <- get.meta(.obj = adata,
                 .sample.var = "sample_id")

# Use with get.cells
cells <- get.cells(.exprs = seurat.obj,
                   .meta = meta,
                   .sample.var = "sample_id")
} # }