% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/deconvo_tme.R
\name{deconvo_xcell}
\alias{deconvo_xcell}
\title{Deconvolve Immune Microenvironment Using xCell}
\usage{
deconvo_xcell(eset, project = NULL, arrays = FALSE)
}
\arguments{
\item{eset}{Gene expression matrix with HGNC gene symbols as row names and
samples as columns.}

\item{project}{Optional project name to add as `ProjectID` column.
Default is `NULL`.}

\item{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`.
}
\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.
}
\examples{
\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)
}
}
}
\author{
Dongqiang Zeng
}
