Deconvolve bulk counts with MuSiC

Usage

deconv_music(
  x,
  experiment,
  sc_reference,
  clusters = "cell_type",
  samples = "sample_id",
  assay = "counts",
  ...,
  reference_assay = NULL
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
sc_reference: Single-cell reference accepted by MuSiC::music_prop().
clusters: Cell-type annotation column in the reference. The default matches the canonical column created by deconv_reference().
samples: Sample identifier column in the reference. The default matches the canonical column created by deconv_reference().
assay: Assay name or one-based assay index.
...: Additional arguments passed to MuSiC::music_prop().
reference_assay: Raw-count assay in sc_reference. NULL selects counts, or the sole assay when no counts assay is present.

Value

The native MuSiC result list. Its weighted estimates are cell-type proportions; they are not on the same scale as xCell enrichment scores.