build_model_dwls: Signature matrix creation with DWLS using genes identified by...

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

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

Description

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

Usage

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.

PelzKo/immunedeconv2 documentation built on Feb. 12, 2025, 4:16 p.m.