dot-bisque_patched_model: Calculates the signature model with bisque

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

Calculates the signature model with bisque

Description

Calculates the signature model with bisque

Usage

.bisque_patched_model(
  single_cell_object,
  cell_type_annotations,
  batch_ids,
  old_cpm = TRUE,
  verbose = FALSE
)

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.
batch_ids	A vector of the ids of the samples or individuals.
old_cpm	Prior to version 1.0.4 (updated in July 2020), the package converted counts to CPM after subsetting the marker genes. Github user randel pointed out that the order of these operations should be switched. Thanks randel! This option is provided for replication of older BisqueRNA but should be enabled, especially for small marker gene sets. We briefly tested this change on the cortex and adipose datasets. The original and new order of operations produce estimates that have an average correlation of 0.87 for the cortex and 0.84 for the adipose within each cell type.
verbose	Whether to produce an output on the console.

Value

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

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