MCPcounter.estimate: MCP-counter Cell Population Abundance Estimation

In IOBR: Immune Oncology Biological Research

MCP-counter Cell Population Abundance Estimation

Description

Estimates the abundance of different immune and stromal cell populations using the MCP-counter method. Works with various gene identifiers including Affymetrix probesets, HUGO gene symbols, Entrez IDs, and Ensembl IDs.

Usage

MCPcounter.estimate(
  expression,
  featuresType = c("affy133P2_probesets", "HUGO_symbols", "ENTREZ_ID", "ENSEMBL_ID"),
  probesets = read.table(system.file("extdata/probesets.txt", package = "IOBR"), sep =
    "\t", stringsAsFactors = FALSE, colClasses = "character"),
  genes = read.table(system.file("extdata/genes.txt", package = "IOBR"), sep = "\t",
    stringsAsFactors = FALSE, header = TRUE, colClasses = "character", check.names =
    FALSE)
)

Arguments

expression	Matrix or data.frame with features in rows and samples in columns.
featuresType	Type of identifiers for expression features. Options: "affy133P2_probesets", "HUGO_symbols", "ENTREZ_ID", "ENSEMBL_ID". Default is "affy133P2_probesets".
probesets	Probesets data table. Default loads from GitHub.
genes	Genes data table. Default loads from GitHub.

Value

Matrix with cell populations in rows and samples in columns.

Author(s)

Etienne Becht

Examples

expr <- matrix(runif(1000), nrow = 100, ncol = 10)
rownames(expr) <- paste0("Gene", 1:100)
estimates <- MCPcounter.estimate(expr, featuresType = "HUGO_symbols")

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