Build a reference signature

Build_model calculates a reference signature from annotated scRNA-seq expression data

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

cell_type_col

Name of the annotation column containing cell type information

method

Signature calculation Algorithm

verbose

Display more information on console

spatial_obj

SpatialExperiment, required for SPOTlight

batch_id_col

column of singleCellExperiment containing batch ids

assay_sc

assay of single cell object to use

assay_sp

assay of spatial object to use

...

additional parameters passed to the functions

Value

cell-type specific expression signature