Create a new Seurat object from a matrix. — initialize_seurat

For an RNA assay the per-cell QC metrics are added at the same time: pct_mito/pct_ribo/ pct_hb (via add_gene_class_percent()), plus detected_genes and total_counts as clearer aliases of nFeature_RNA/nCount_RNA, and sample_name as a clearer alias of orig.ident. All six are metadata columns as soon as the object exists, so plot_metrics_distribution() (which takes its metrics explicitly, no default) and plot_metrics_correlations() can use any of them without further preparation.

Usage

initialize_seurat_object(
  counts_matrix,
  assay = "RNA",
  min_cells = 1,
  min_genes = 1,
  project = "proj",
  log_file = NULL
)

Arguments

counts_matrix: A matrix of raw counts.
assay: Seurat assay to add the data to.
min_cells: Include genes/features detected in at least this many cells.
min_genes: Include cells where at least this many genes/features are detected.
project: Project name for Seurat object.
log_file: Filename for the logfile.

Value

Seurat object.