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

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

\item{tumor}{Logical: tumor samples. Must be specified.}

\item{arrays}{Logical: microarray data. Must be specified.}

\item{scale_mrna}{Logical: correct for mRNA content. Must be specified.}
}
\value{
Data frame with quanTIseq cell fractions. Columns suffixed with
  `_quantiseq`.
}
\description{
quanTIseq deconvolution for RNA-seq immune cell fractions.
}
\examples{
\dontrun{
quantiseq_data <- load_data("quantiseq_data")
if (!is.null(quantiseq_data)) {
  set.seed(123)
  n_sig <- nrow(quantiseq_data$TIL10_signature)
  sim_eset <- matrix(rnorm(n_sig * 2), n_sig, 2)
  rownames(sim_eset) <- rownames(quantiseq_data$TIL10_signature)
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_quantiseq(eset = sim_eset, project = "Example", tumor = TRUE,
                              arrays = FALSE, scale_mrna = FALSE)
  if (!is.null(result)) head(result)
}
}
}
\author{
Dongqiang Zeng
}
