deconvo_mcpcounter: Deconvolve Immune Microenvironment Using MCP-Counter
In IOBR: Immune Oncology Biological Research

deconvo_mcpcounter

R Documentation

Deconvolve Immune Microenvironment Using MCP-Counter

Description

Estimates immune cell abundances using MCP-counter.

Usage

deconvo_mcpcounter(eset, project = NULL)

Arguments

`eset`	Gene expression matrix with HGNC symbols as row names.
`project`	Optional project name. Default is 'NULL'.

Value

Data frame with MCP-counter scores. Columns suffixed with '_MCPcounter'.

Author(s)

Dongqiang Zeng

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_mcpcounter(eset = sim_eset, project = "TCGA-STAD")
  if (!is.null(result)) head(result)
}

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