Deconvolute Omnideconv — deconvolute_omnideconv • spacedeconv

Deconvolute Omnideconv

Usage

deconvolute_omnideconv(
  spatial_obj,
  signature = NULL,
  method = NULL,
  single_cell_obj = NULL,
  cell_type_col = "cell_ontology_class",
  batch_id_col = NULL,
  assay_sc = "counts",
  assay_sp = "counts",
  verbose = FALSE,
  result_name = NULL,
  ...
)

Arguments

spatial_obj: SpatialExperiment
signature: A signature matrix
method: omnideconv deconvolution method, see omnideconv::deconvolution_methods() for details
single_cell_obj: Needed for MOMF and Bisque, either a matrix with cell type annotations in the cell_type_annotations parameter or a singleCellExperiment / AnnData where the cell_type_column_name specifies the corresponding column where the cell type annotation is located in the object
cell_type_col: column name of single_cell_obj where cell type information is found
batch_id_col: column name of single_cell_obj where batch ids can be found
assay_sc: single cell assay to use
assay_sp: spatial assay to use
verbose: Whether to produce output on the console
result_name: token to identify deconvolution results in object, default = selected deconvolution method
...: Additional parameters, passed to the selected method