RCTD Deconvolution

Usage

deconvolute_rctd(
  single_cell_obj,
  cell_type_col,
  spatial_obj,
  assay_sc = "counts",
  assay_sp = "counts",
  n_umi_sc = NULL,
  n_umi_sp = NULL,
  n_cores = NULL,
  result_name = "rctd"
)

Arguments

single_cell_obj: SingleCellExperiment
cell_type_col: Column containting cell type annotation
spatial_obj: SpatialExperiment
assay_sc: single cell assay to use
assay_sp: spatial assay to use
n_umi_sc: (optional) named list of umi counts for each cell
n_umi_sp: (optional) named list of umi counts for each spot
n_cores: Number of CPU cores to use for the calculation, NULL = use all cores
result_name: token to identify deconvolution results in object, default = "rctd"