% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/iobr_deconvo_pipeline.R
\name{iobr_deconvo_pipeline}
\alias{iobr_deconvo_pipeline}
\title{Tumor Microenvironment (TME) Deconvolution Pipeline}
\usage{
iobr_deconvo_pipeline(
  eset,
  project,
  array,
  tumor_type,
  path = NULL,
  permutation = 1000
)
}
\arguments{
\item{eset}{Numeric matrix. Gene expression (TPM/log scale) with genes in rows.}

\item{project}{Character. Project name (used in output naming).}

\item{array}{Logical. Whether data originated from an array platform. Affects deconvolution choices.}

\item{tumor_type}{Character. Tumor type code (e.g., "stad") used by certain methods.}

\item{path}{Character. Output directory. Default is NULL (uses tempdir()).}

\item{permutation}{Integer. Number of permutations for CIBERSORT (and similar). Default is 1000.}
}
\value{
Data frame integrating cell fractions and signature scores (also writes intermediate outputs to disk).
}
\description{
Executes an integrated TME analysis on a gene expression matrix: performs
immune/stromal cell deconvolution using multiple algorithms, computes
signature scores, and aggregates results. Designed for exploratory
immunogenomic profiling.
}
\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 <- iobr_deconvo_pipeline(
  eset = eset, project = "STAD",
  array = FALSE, tumor_type = "stad",
  path = tempdir(), permutation = 10
)
}
}
\author{
Dongqiang Zeng
}
