% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/deconvo_tme.R
\name{deconvo_cibersort}
\alias{deconvo_cibersort}
\title{Deconvolve Using CIBERSORT}
\usage{
deconvo_cibersort(
  eset,
  project = NULL,
  arrays = FALSE,
  perm = 1000,
  absolute = FALSE,
  abs_method = "sig.score",
  parallel = FALSE,
  num_cores = 2,
  seed = NULL
)
}
\arguments{
\item{eset}{Expression matrix with gene symbols as row names.}

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

\item{arrays}{Logical: optimized for microarray data. Default is `FALSE`.}

\item{perm}{Permutations for statistical analysis. Default is 1000.}

\item{absolute}{Logical: run in absolute mode. Default is `FALSE`.}

\item{abs_method}{Method for absolute mode: `"sig.score"` or `"no.sumto1"`.
Default is `"sig.score"`.}

\item{parallel}{Enable parallel execution. Default is `FALSE`.}

\item{num_cores}{Number of cores for parallel mode. Default is 2.}

\item{seed}{Random seed for reproducibility. Default is `NULL`.}
}
\value{
Data frame with CIBERSORT cell fractions. Columns suffixed with `_CIBERSORT`.
}
\description{
CIBERSORT is freely available to academic users. License and binary can be
obtained from https://cibersortx.stanford.edu.
}
\examples{
\dontrun{
lm22 <- load_data("lm22")
if (!is.null(lm22)) {
  set.seed(123)
  sim_eset <- matrix(rnorm(nrow(lm22) * 2), nrow(lm22), 2)
  rownames(sim_eset) <- rownames(lm22)
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_cibersort(eset = sim_eset, project = "TCGA-STAD", perm = 10)
  if (!is.null(result)) head(result)
}
}
}
\author{
Dongqiang Zeng
}
