Deconvolute using BASE and a custom signature matrix

Deconvolute using BASE and a custom signature matrix

deconvolute_base_custom(
  gene_expression_matrix,
  signature_matrix,
  n_permutations = 100,
  log10 = TRUE
)

Arguments

gene_expression_matrix

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

signature_matrix

a m x l matrix with m genes and l cell types. Data should be non normalized, as the normalization wil be done in the construction of the compendium (internal structure)

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.