Deconvolute with RCTD — deconvolute

Runs the RCTD workflow and returns a deconvolution matrix with column names prefixed by result_name.

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 containing cell type labels.
spatial_obj: SpatialExperiment.
assay_sc: Single-cell assay to use.
assay_sp: Spatial assay to use.
n_umi_sc: Optional named vector of UMI counts per cell.
n_umi_sp: Optional named vector of UMI counts per spot.
n_cores: Number of CPU cores to use; NULL uses all cores.
result_name: Prefix used to label result columns (default: "rctd").