Deconvolute using BASE

Source: R/mouse_deconvolution_methods.R

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

deconvolute_base_algorithm(
  gene_expression_matrix,
  n_permutations = 100,
  log10 = TRUE,
  combine_cells = TRUE
)

Arguments

gene_expression_matrix

a m x n matrix with m genes and n samples. Data should be TPM normalized and log10 scaled.

n_permutations

the number of permutations of each sample expression to generate. These are used to normalize the results.

log10

logical. if TRUE, log10 transforms the expression matrix.

combine_cells

logical. This method estimates several cell types (~180). If TRUE (default), these are combined into 19 major immune-stromal cell types.