Merge multiple Seurat objects into one.

Merges a list of Seurat objects, rejoins the split layers that Seurat 5 leaves behind, and removes genes that are detected in too few cells. Features of the non-RNA assays (such as ADT and HTO) are always kept.

Usage

merge_seurat_objects(seurat_object_list, min_cells = NULL, log_file = NULL)

Arguments

seurat_object_list

List of Seurat objects and/or analysis directory paths (mixing both is fine).

min_cells

Keep genes detected in at least this many cells. If NULL, 10 is used, or 0.1% of the cells when there are more than 50,000 of them.

log_file

Filename for the log file.

Value

A merged Seurat object.

Details

Elements of seurat_object_list may be Seurat objects, or paths to an analysis directory containing a seurat_obj.qs2 (as written by the CLI). Which one it is does not matter to the caller: this function resolves each element to an object first.

Once every input is an object, this function strips each one's own reductions, scaled data, and clustering columns before merging. A per-sample PCA, tSNE/UMAP, or clustering — written by create_seurat_object()/cluster_seurat_object() — is meaningless once merged. normalize_counts()/run_pca() recompute all of it downstream anyway.

Writes metrics-distribution.png, a per-sample QC violin plot, to the working directory.