deconvo_cibersort: Deconvolve Using CIBERSORT
In IOBR: Immune Oncology Biological Research

deconvo_cibersort

R Documentation

Deconvolve Using CIBERSORT

Description

CIBERSORT is freely available to academic users. License and binary can be obtained from https://cibersortx.stanford.edu.

Usage

deconvo_cibersort(
  eset,
  project = NULL,
  arrays = FALSE,
  perm = 1000,
  absolute = FALSE,
  abs_method = "sig.score",
  parallel = FALSE,
  num_cores = 2,
  seed = NULL
)

Arguments

`eset`	Expression matrix with gene symbols as row names.
`project`	Optional project name. Default is 'NULL'.
`arrays`	Logical: optimized for microarray data. Default is 'FALSE'.
`perm`	Permutations for statistical analysis. Default is 1000.
`absolute`	Logical: run in absolute mode. Default is 'FALSE'.
`abs_method`	Method for absolute mode: '"sig.score"' or '"no.sumto1"'. Default is '"sig.score"'.
`parallel`	Enable parallel execution. Default is 'FALSE'.
`num_cores`	Number of cores for parallel mode. Default is 2.
`seed`	Random seed for reproducibility. Default is 'NULL'.

Value

Data frame with CIBERSORT cell fractions. Columns suffixed with '_CIBERSORT'.

Author(s)

Dongqiang Zeng

Examples

## Not run: 
lm22 <- load_data("lm22")
if (!is.null(lm22)) {
  set.seed(123)
  sim_eset <- matrix(rnorm(nrow(lm22) * 2), nrow(lm22), 2)
  rownames(sim_eset) <- rownames(lm22)
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_cibersort(eset = sim_eset, project = "TCGA-STAD", perm = 10)
  if (!is.null(result)) head(result)
}

## End(Not run)

IOBR documentation built on May 30, 2026, 5:07 p.m.