Extract Sample-Level Metadata from HDF5AnnData Object

Extracts sample-wise metadata from an HDF5-backed AnnData object by identifying which obs columns have consistent values within each sample. Returns a data frame suitable for setup.tdr.obj(.meta = ...).

Usage

get.meta.HDF5AnnData(.h5ad.obj, .sample.var, .verbose = TRUE)

Arguments

.h5ad.obj

An HDF5AnnData object (created via anndataR::read_h5ad(..., backend = "HDF5AnnData")).

.sample.var

Character: column name in .h5ad.obj$obs 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 from .sample.var.

Details

AnnData objects store cell-level annotations in obs. This function:

1. Reads obs as a data frame

2. Groups by .sample.var

3. Identifies columns with unique values within each sample (sample-level)

4. Excludes varying columns (cell-level) with warning

5. Returns one row per sample

See also

get.meta for automatic format detection, get.meta.Seurat for Seurat objects, get.meta.SCE for SingleCellExperiment objects

Examples

if (FALSE) { # \dontrun{
adata <- anndataR::read_h5ad("data.h5ad", backend = "HDF5AnnData")
meta <- get.meta.HDF5AnnData(.h5ad.obj = adata,
                             .sample.var = "sample_id")
} # }