build_model_bseqsc: Calculates the signature model with BSeq-sc

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

Calculates the signature model with BSeq-sc

Description

Calculates the signature model with BSeq-sc

Usage

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.

Value

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

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