deconvolute_base_algorithm: Deconvolute using BASE

In grst/immunedeconv: Methods for immune cell deconvolution

Deconvolute using BASE

Description

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

Usage

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.

grst/immunedeconv documentation built on Nov. 10, 2023, 1:33 a.m.