% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/timer.R
\name{deconvolute_timer.default}
\alias{deconvolute_timer.default}
\title{Deconvolute Tumor Microenvironment Using TIMER}
\usage{
deconvolute_timer.default(args)
}
\arguments{
\item{args}{List or environment containing parameters:
\describe{
  \item{outdir}{Character. Output directory path.}
  \item{batch}{Character. File containing paths to expression data and
    cancer types.}
}}
}
\value{
Matrix of abundance scores for different immune cell types across
  multiple cancer samples.
}
\description{
Performs deconvolution of the tumor microenvironment using the TIMER
algorithm. Processes multiple cancer datasets, removes batch effects,
and estimates immune cell type abundances.
}
\examples{
\dontrun{
# This example requires actual expression data files
# Create a batch file with paths to expression data and cancer types
batch_file <- "batch.csv"
# batch.csv format: each row contains expression_file_path,cancer_type
# Example content:
# /path/to/exp1.txt,luad
# /path/to/exp2.txt,brca
outdir <- tempdir()
args <- list(outdir = outdir, batch = batch_file)
results <- deconvolute_timer.default(args)
}
}
