Deconvolution with spacedeconv — deconvolute • spacedeconv

Runs the selected deconvolution method on a SpatialExperiment. Methods may use a precomputed signature (from build_model()) or build internally. See spacedeconv::deconvolution_methods for the full list of methods.

Usage

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

Arguments

spatial_obj: A SpatialExperiment to deconvolute.
signature: Gene expression signature matrix (if required by the method).
single_cell_obj: A SingleCellExperiment with reference cells (if required).
cell_type_col: Column name in single_cell_obj containing cell types.
method: Deconvolution method; one of spacedeconv::deconvolution_methods.
batch_id_col: Batch ID column in single_cell_obj (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 the input SpatialExperiment with results added to colData; otherwise return the result matrix.
verbose: Print extra progress information.
...: Further parameters passed to the selected method.

Value

Deconvolution results as a matrix or a SpatialExperiment.