Build a Reference Signature
build_model.Rd
Computes a cell-type signature from annotated scRNA-seq data or
dispatches to a method-specific builder. The resulting signature
can be passed to
deconvolute() as the
signature argument. Some methods (e.g., CARD, DOT,
immunedeconv) do not produce a signature and return
NULL.
Usage
build_model(
single_cell_obj,
cell_type_col = "cell_ontology_class",
method = NULL,
verbose = FALSE,
spatial_obj = NULL,
batch_id_col = NULL,
assay_sc = "counts",
assay_sp = "counts",
...
)Arguments
- single_cell_obj
Single-cell object with cell type annotations.
- cell_type_col
Column name containing cell type labels.
- method
-
Signature method; one of
spacedeconv::deconvolution_methods. - verbose
Print extra progress information.
- spatial_obj
SpatialExperiment; required for SPOTlight.
- batch_id_col
-
Batch ID column in the single-cell object (used by some methods).
- assay_sc
Single-cell assay to use (default: "counts").
- assay_sp
Spatial assay to use (default: "counts").
- ...
-
Additional parameters passed to the selected method.