Build Model and Deconvolute in one step

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 containing reference data to build the model
spatial_obj: SpatialExperiment to be deconvoluted
method: deconvolution method
cell_type_col: column of single_cell_obj containing cell type information
batch_id_col: column of SpatialObject containing batch_id information
assay_sc: the assay of the single cell object to use, default = "counts"
assay_sp: the assay of the spatialExperiment to use, default = "counts"
return_object: if true return anotation spatialExperiment, if false return table
verbose: output more information
...: further parameters passed to the selected function