deconvo_tme: Main TME Deconvolution Function

In IOBR: Immune Oncology Biological Research

Main TME Deconvolution Function

Description

Unified interface for multiple TME deconvolution methods.

Usage

deconvo_tme(
  eset,
  project = NULL,
  method = tme_deconvolution_methods,
  arrays = FALSE,
  tumor = TRUE,
  perm = 1000,
  reference,
  scale_reference = TRUE,
  plot = FALSE,
  scale_mrna = TRUE,
  group_list = NULL,
  platform = "affymetrix",
  absolute.mode = FALSE,
  abs.method = "sig.score",
  ...
)

Arguments

eset	Gene expression matrix with HGNC symbols as row names.
project	Optional project name. Default is 'NULL'.
method	Deconvolution method. See [tme_deconvolution_methods].
arrays	Logical: microarray-optimized mode. Default is 'FALSE'.
tumor	Logical: tumor-optimized mode (EPIC). Default is 'TRUE'.
perm	Permutations (CIBERSORT/SVR). Default is 1000.
reference	Custom reference matrix (SVR/lsei).
scale_reference	Logical: scale reference (SVR/lsei).
plot	Logical: generate plots (IPS). Default is 'FALSE'.
scale_mrna	Logical: mRNA correction (quanTIseq/EPIC).
group_list	Cancer types for TIMER (vector).
platform	Platform for ESTIMATE. Default is '"affymetrix"'.
absolute.mode	Logical: absolute mode (CIBERSORT/SVR). Default is 'FALSE'.
abs.method	Absolute mode method. Default is '"sig.score"'.
...	Additional arguments passed to method.

Value

Tibble with cell fractions and 'ID' column.

Author(s)

Dongqiang Zeng, Rongfang Shen

References

1. Newman et al. (2015). Robust enumeration of cell subsets from tissue expression profiles. Nature Methods.

2. Vegesna et al. (2013). Inferring tumour purity and stromal/immune cell admixture. Nature Communications.

3. Finotello et al. (2019). Molecular and pharmacological modulators of the tumor immune contexture. Genome Medicine.

4. Li et al. (2016). Comprehensive analyses of tumor immunity. Genome Biology.

5. Charoentong et al. (2017). Pan-cancer Immunogenomic Analyses. Cell Reports.

6. Becht et al. (2016). Estimating population abundance of tissue-infiltrating immune cells. Genome Biology.

7. Aran et al. (2017). xCell: digitally portraying tissue cellular heterogeneity. Genome Biology.

8. Racle et al. (2017). Simultaneous enumeration of cancer and immune cell types. ELife.

Examples

mcp_genes <- load_data("mcp_genes")
if (!is.null(mcp_genes)) {
  set.seed(123)
  sim_eset <- matrix(rnorm(nrow(mcp_genes) * 3), nrow(mcp_genes), 3)
  rownames(sim_eset) <- mcp_genes$`HUGO symbols`
  colnames(sim_eset) <- paste0("Sample", 1:3)
  
  # Run deconvolution
  result <- deconvo_tme(eset = sim_eset, method = "mcpcounter")
  if (!is.null(result)) head(result)
}

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