% 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{
\donttest{
eset_stad <- load_data("eset_stad")
anno_grch38 <- load_data("anno_grch38")
eset <- anno_eset(eset = eset_stad, annotation = anno_grch38, probe = "id")
xcell_result <- deconvo_xcell(eset = eset[, 1:3], project = "TCGA-STAD")
head(xcell_result)[, 1:5]
}
}
\author{
Dongqiang Zeng
}
