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Extract Sample-Level Metadata from Seurat v5 Object

Source: R/preprocess.R
get.meta.Seurat5.Rd

Extracts sample-wise metadata from a Seurat v5 object by identifying which metadata columns have consistent values within each sample (sample-level variables). Cell-level variables are excluded with a warning. Returns a data frame suitable for setup.tdr.obj(.meta = ...).

Usage

get.meta.Seurat5(.seurat.obj, .sample.var, .verbose = TRUE)

Arguments

.seurat.obj

Seurat v5 object with cell-level metadata in @meta.data.

.sample.var

Character: column name in .seurat.obj@meta.data 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

This function automatically distinguishes sample-level from cell-level metadata:

  • Sample-level: Variables with identical values for all cells within each sample (e.g., Condition, Batch, Treatment). These are kept.

  • Cell-level: Variables that vary between cells in the same sample (e.g., nCount_RNA, percent.mt, cluster). These are excluded with a warning.

The .sample.var column is always included. Only distinct rows are returned (one per sample).

Useful when you've stored experimental design information in the Seurat object and want to extract it for tinydenseR analysis.

See also

get.meta for automatic format detection, get.meta.Seurat for Seurat v4, get.cells.Seurat5 for extracting count data

Examples

if (FALSE) { # \dontrun{
# Assuming Seurat object has sample metadata
meta <- get.meta.Seurat5(.seurat.obj = seurat.obj,
                         .sample.var = "sample_id")

# Use with get.cells
cells <- get.cells.Seurat5(.seurat.obj = seurat.obj,
                           .meta = meta,
                           .sample.var = "sample_id")
} # }