Deconvolve Immune Microenvironment Using xCell

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

Dongqiang Zeng

Examples

if (FALSE) { # \dontrun{
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)
}
} # }