% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/result_classes.R
\docType{class}
\name{dnaEPICO_svaEnmix-class}
\alias{dnaEPICO_svaEnmix-class}
\alias{dnaEPICO_svaEnmix}
\title{Result class returned by svaEnmix}
\description{
Objects of class \code{'dnaEPICO_svaEnmix'} are list-based results returned by
\code{\link[=svaEnmix]{svaEnmix()}}. They collect the loaded inputs, surrogate-variable results,
association-analysis summaries, and optional file outputs.
}
\section{Structure}{

\describe{
\item{targets}{Phenotype table read from \code{phenoFile} after any optional row
subsetting.}
\item{RGSet}{Loaded \code{RGChannelSet} with sample names reset to match
\code{targets}.}
\item{svaData}{Object returned by \code{\link[=estimateSvaEnmixControls]{estimateSvaEnmixControls()}}.}
\item{mergedPheno}{Phenotype table returned by \code{\link[=mergeSvaTargetsEnmix]{mergeSvaTargetsEnmix()}}
after surrogate variables were appended.}
\item{analysisData}{Object returned by \code{\link[=analyzeSvaEnmix]{analyzeSvaEnmix()}}.}
\item{plotFiles}{Named list of TIFF output paths for the SVA figures when
\code{saveOutputs = TRUE}, otherwise \code{NULL} entries for plots not written.}
\item{savedFiles}{Object returned by \code{\link[=writeSvaEnmixOutputs]{writeSvaEnmixOutputs()}} when
\code{saveOutputs = TRUE}, otherwise \code{NULL}.}
\item{logFile}{Resolved path to the optional log file, or \code{NULL} when
logging was disabled.}
}
}

\seealso{
\code{\link[=svaEnmix]{svaEnmix()}}
}
