% 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{
eset_stad <- load_data("eset_stad")
anno_grch38 <- load_data("anno_grch38")
eset <- anno_eset(eset = eset_stad, annotation = anno_grch38, probe = "id")
eset <- eset[1:500, 1:3]
\donttest{
res <- deconvo_quantiseq(
  eset = eset, project = "stad", tumor = TRUE,
  arrays = FALSE, scale_mrna = FALSE
)
head(res)
}
}
\author{
Dongqiang Zeng
}
