deconvolute_cibersort_custom: Deconvolute using CIBERSORT or CIBERSORT abs and a custom...

In grst/immunedeconv: Methods for immune cell deconvolution

Deconvolute using CIBERSORT or CIBERSORT abs and a custom signature matrix.

Description

Deconvolute using CIBERSORT or CIBERSORT abs and a custom signature matrix.

Usage

deconvolute_cibersort_custom(
  gene_expression_matrix,
  signature_matrix,
  QN = FALSE,
  absolute = FALSE,
  abs_method = "sig.score",
  ...
)

Arguments

gene_expression_matrix	a m x n matrix with m genes and n samples
signature_matrix	a m x l matrix with m genes and l cell types. The matrix should contain only a subset of the genes useful for the analysis.
QN	boolean. Wheter to quantile normalize the data. Data should be normalized when the signature matrix is derived from different studies/sample batches
absolute	Set to TRUE for CIBERSORT absolute mode.
abs_method	Choose method to compute absolute score (only if absolute=TRUE).
...	passed through to the original CIBERSORT function. A native argument takes precedence over an immunedeconv argument (e.g. QN takes precedence over arrays). Documentation is not publicly available. Log in to the CIBERSORT website for details.

Note

the gene expression and the signature matrix should be provided in the same normalization

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