% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/deconvo_tme.R
\name{deconvo_timer}
\alias{deconvo_timer}
\title{Deconvolve Using TIMER}
\usage{
deconvo_timer(eset, project = NULL, indications = NULL)
}
\arguments{
\item{eset}{Gene expression matrix.}

\item{project}{Optional project name. Default is `NULL`.}

\item{indications}{Cancer type for each sample (e.g., `"brca"`, `"stad"`).
Must match number of columns in `eset`.}
}
\value{
Data frame with TIMER cell fractions. Columns suffixed with `_TIMER`.
}
\description{
TIMER deconvolution for cancer-specific immune estimation.
}
\examples{
\dontrun{
immune <- load_data("immuneCuratedData")
cancer_genes <- load_data("cancer_type_genes")
if (!is.null(immune) && !is.null(cancer_genes)) {
  set.seed(123)
  genes <- unique(c(head(rownames(immune$genes), 100), cancer_genes[["stad"]]))
  sim_eset <- matrix(rnorm(length(genes) * 2), length(genes), 2)
  rownames(sim_eset) <- genes
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_timer(eset = sim_eset, project = "TCGA-STAD",
                          indications = rep("stad", 2))
  if (!is.null(result)) head(result)
}
}
}
\author{
Dongqiang Zeng
}
