deconvo_xcell: Deconvolve Immune Microenvironment Using xCell
In IOBR: Immune Oncology Biological Research

deconvo_xcell

R Documentation

Deconvolve Immune Microenvironment Using xCell

Description

Estimates immune cell fractions using the xCell algorithm. xCell provides cell type enrichment scores for 64 immune and stromal cell types from gene expression data.

Usage

deconvo_xcell(eset, project = NULL, arrays = FALSE)

Arguments

`eset`	Gene expression matrix with HGNC gene symbols as row names and samples as columns.
`project`	Optional project name to add as 'ProjectID' column. Default is 'NULL'.
`arrays`	Logical indicating microarray data ('TRUE') or RNA-seq ('FALSE'). Default is 'FALSE'.

Value

Data frame with xCell enrichment scores. Cell type columns are suffixed with '_xCell'.

Author(s)

Dongqiang Zeng

Examples

## Not run: 
xcell <- load_data("xCell.data")
if (!is.null(xcell)) {
  set.seed(123)
  sim_eset <- matrix(rnorm(length(xcell$genes) * 2), length(xcell$genes), 2)
  rownames(sim_eset) <- xcell$genes
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_xcell(eset = sim_eset, project = "TCGA-STAD")
  if (!is.null(result)) head(result)
}

## End(Not run)

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