Calculates the signature model with BSeq-sc

build_model_bseqsc(
  single_cell_object,
  cell_type_annotations,
  markers,
  batch_ids,
  ct_scale = TRUE,
  limit = TRUE
)

Arguments

single_cell_object: A matrix with the single-cell data. Rows are genes, columns are samples. Row and column names need to be set.
cell_type_annotations: A vector of the cell type annotations. Has to be in the same order as the samples in single_cell_object.
markers: Named list of cell type marker genes with the names being the cell type. The type of gene identifiers must be the same as the ones used as feature/row names in the single_cell_object.
batch_ids: A vector of the ids of the samples or individuals.
ct_scale: logical that indicates if the single cell expresson profiles should be rescaled according to their cell type average total count.
limit: logical that indicates if the returned basis matrix should only contain cell types listed in markers.

The signature matrix. Rows are genes, columns are cell types.