Build Model and Deconvolute in One Step — build_and

Convenience wrapper that builds a signature with build_model() and then calls deconvolute() using the same inputs.

Usage

build_and_deconvolute(
  single_cell_obj,
  spatial_obj,
  method = NULL,
  cell_type_col = "cell_ontology_class",
  batch_id_col = NULL,
  assay_sc = "counts",
  assay_sp = "counts",
  return_object = TRUE,
  verbose = FALSE,
  ...
)

Arguments

single_cell_obj: Single-cell object used to build the signature.
spatial_obj: SpatialExperiment to deconvolute.
method: Deconvolution method; one of spacedeconv::deconvolution_methods.
cell_type_col: Column in single_cell_obj with cell type labels.
batch_id_col: Batch ID column (used by some methods).
assay_sc: Single-cell assay to use (default: "counts").
assay_sp: Spatial assay to use (default: "counts").
return_object: If TRUE, return an annotated SpatialExperiment; otherwise return the result matrix.
verbose: Print extra progress information.
...: Additional parameters passed to the selected methods.