% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/dnaEPICO-package.R
\docType{package}
\name{dnaEPICO}
\alias{dnaEPICO-package}
\alias{dnaEPICO}
\title{dnaEPICO: DNA methylation preprocessing and modeling workflows}
\description{
The \code{dnaEPICO} package provides a structured workflow for preprocessing and
analyzing Illumina DNA methylation array data, including quality control,
normalization, cell-type estimation, surrogate-variable analysis, phenotype
preparation, CpG-wise generalised linear models, longitudinal mixed-effects
models using \code{lmerTest}/\code{lme4} or \code{nlme} with optional residual correlation
structures, and interactive web reporting.
}
\details{
The package supports two complementary usage styles:
\itemize{
\item interactive use, where functions return structured in-memory result
objects for inspection and composition; and
\item file-based pipeline use, where the same functions can write logs,
plots, tables, and serialized objects when \code{saveOutputs = TRUE}.
}

The main high-level entry points are:
\itemize{
\item \code{\link[=preprocessingMinfiEwasWater]{preprocessingMinfiEwasWater()}}
\item \code{\link[=svaEnmix]{svaEnmix()}}
\item \code{\link[=preprocessingPheno]{preprocessingPheno()}}
\item \code{\link[=methylationGLM]{methylationGLM()}}
\item \code{\link[=methylationLME]{methylationLME()}}
\item \code{\link[=dnamReport]{dnamReport()}}
}
}
\seealso{
Useful links:
\itemize{
  \item \url{https://github.com/paulYRP/dnaEPICO}
  \item Report bugs at \url{https://github.com/paulYRP/dnaEPICO/issues}
}

}
\author{
\strong{Maintainer}: Paul Ruiz \email{ruizpint@qut.edu.au} (\href{https://orcid.org/0009-0007-6714-3566}{ORCID})

}
\keyword{package}
