deconvolute_base_custom: Deconvolute using BASE and a custom signature matrix

In grst/immunedeconv: Methods for immune cell deconvolution

Deconvolute using BASE and a custom signature matrix

Description

Deconvolute using BASE and a custom signature matrix

Usage

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.

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