% 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{
eset_stad <- load_data("eset_stad")
anno_grch38 <- load_data("anno_grch38")
eset <- anno_eset(eset = eset_stad, annotation = anno_grch38, probe = "id")
\donttest{
res <- deconvo_timer(
  eset = eset, project = "stad",
  indications = rep("stad", ncol(eset))
)
head(res)
}
}
\author{
Dongqiang Zeng
}
