Construct a single-cell deconvolution reference — deconv

Builds the canonical SingleCellExperiment reference accepted directly by deconv_music() and deconv_bayesprism(). This helper only standardizes a user-supplied single-cell count matrix and its metadata; it does not provide or simulate a biological reference.

Usage

deconv_reference(
  counts,
  cell_data,
  cell_type,
  sample,
  cell_state = NULL,
  assay_name = "counts"
)

Arguments

counts: Raw integer count matrix with genes in rows and cells in columns. Dense matrices and sparse Matrix objects are accepted without densifying the latter. Complete, unique gene and cell names are required.
cell_data: Cell-level metadata with row names containing every count matrix cell name exactly once. Rows are aligned by cell name.
cell_type, sample: A column name in cell_data, or a named vector with one non-missing label per cell. Values are stored in the canonical cell_type and sample_id columns.
cell_state: Optional cell-state column name or named vector. When supplied, values are stored in the canonical cell_state column.
assay_name: Name used for the raw-count assay.

Value

A SingleCellExperiment with aligned cell metadata.