Cell types obtained with this method can be further reduced with the map_result_to_celltypes function, using 'DCQ' as the method

deconvolute_dcq(
  gene_expression_matrix,
  ref_samples = NULL,
  n_repeats = 10,
  combine_cells = TRUE,
  ...
)

Arguments

gene_expression_matrix

a m x n matrix with m genes and n samples

ref_samples

a vector containing the names of the samples to be used to standardize the expressions. If NULL, all the samples are used.

n_repeats

the number of models to generate. Predicted cell quantities will then be averaged.

combine_cells

logical. This method estimates several cell types (~200). If TRUE (default), these are combined into 19 major immune-stromal cell types.

...

passed through to original quantiseq method. A native argument takes precedence over an immunedeconv argument