deconvolute_cibersort: Deconvolute using CIBERSORT or CIBERSORT abs.

In grst/immunedeconv: Methods for immune cell deconvolution

Deconvolute using CIBERSORT or CIBERSORT abs.

Description

Deconvolute using CIBERSORT or CIBERSORT abs.

Usage

deconvolute_cibersort(
  gene_expression_matrix,
  arrays,
  absolute = FALSE,
  abs_method = "sig.score",
  ...
)

Arguments

gene_expression_matrix	a m x n matrix with m genes and n samples
arrays	Set to TRUE if working with Microarray data instead of RNA-seq. As recommended by the authors, quantile normalization will be enabled for Microarrays and disabled for RNAseq.
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.

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