Signature matrix creation with DWLS using genes identified by a differential analysis

build_model_dwls(
  single_cell_object,
  cell_type_annotations,
  dwls_method = c("mast", "seurat", "mast_optimized"),
  path = NULL,
  verbose = FALSE,
  diff_cutoff = 0.5,
  pval_cutoff = 0.01,
  ncores = 1
)

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.
dwls_method: The method used to create the signature matrix. Options are "mast", "mast_optimized" and "seurat"
path: The path where the generated files will be saved. If path=NULL, the generated files will be discarded.
verbose: Whether to produce an output on the console.
diff_cutoff: Cutoff to determine the FC-limit. How low can the lowest fold change be to still be considered differentially expressed?
pval_cutoff: Cutoff to determine the pVal-limit. How high can the highest p-Value be to still be considered statistically significant?
ncores: Choose how many core to use for signature calculation. Is only applied when using 'mast' as method.

Value

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