% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/xCell.R
\name{xCellAnalysis}
\alias{xCellAnalysis}
\title{The xCell Analysis Pipeline}
\usage{
xCellAnalysis(
  expr,
  signatures = NULL,
  genes = NULL,
  spill = NULL,
  rnaseq = TRUE,
  file.name = NULL,
  scale = TRUE,
  alpha = 0.5,
  save.raw = FALSE,
  cell.types.use = NULL
)
}
\arguments{
\item{expr}{Gene expression data matrix with row names as gene symbols and
columns as samples.}

\item{signatures}{GMT object of signatures. If `NULL`, uses xCell defaults.}

\item{genes}{Character vector of genes to use in the analysis. If `NULL`,
uses xCell defaults.}

\item{spill}{Spillover object for adjusting scores. If `NULL`, uses xCell defaults.}

\item{rnaseq}{Logical indicating whether to use RNA-seq (TRUE) or array
(FALSE) spillover parameters. Default is `TRUE`.}

\item{file.name}{Character string for saving scores. Default is `NULL`.}

\item{scale}{Logical indicating whether to use scaling. Default is `TRUE`.}

\item{alpha}{Numeric value to override spillover alpha parameter. Default is `0.5`.}

\item{save.raw}{Logical indicating whether to save raw scores. Default is `FALSE`.}

\item{cell.types.use}{Character vector of cell types to use. If `NULL`, uses
all available cell types. Default is `NULL`.}
}
\value{
A matrix of adjusted xCell scores.
}
\description{
Returns the xCell cell types enrichment scores for tumor microenvironment
deconvolution. Uses ssGSEA-based enrichment analysis with spillover
compensation to estimate cell type proportions from gene expression data.
}
\keyword{internal}
