Deconvolution with spacedeconv — deconvolute • spacedeconv

Perform cell type deconvolution with spacedeconv.

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
signature: Gene Expression Signature
single_cell_obj: A SingleCellExperiment
cell_type_col: Column name of the single_cell_obj where the cell type can be found
method: Deconvolution Method to use, see deconvolution_methods() for a full list of available methods
batch_id_col: column name of batch ids in single cell object
assay_sc: which single cell assay to use for computation
assay_sp: which spatial assay to use for computation
return_object: Return an Object or result Table, TRUE = Object
verbose: display more detailed information
...: Further parameters passed to the selected deconvolution method

Value

The deconvolution result as a table