MCP-counter Cell Population Abundance Estimation

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(url(paste0("https://raw.githubusercontent.com/ebecht/",
    "MCPcounter/master/Signatures/probesets.txt")), sep = "\t", stringsAsFactors =
    FALSE, colClasses = "character"),
  genes = read.table(url(paste0("https://raw.githubusercontent.com/ebecht/",
    "MCPcounter/master/Signatures/genes.txt")), 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

Etienne Becht

Examples

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