% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/dnamReport.R
\name{prepareDnamReportInputs}
\alias{prepareDnamReportInputs}
\title{Prepare inputs for a DNA methylation report}
\usage{
prepareDnamReportInputs(
  outputDir = "reports",
  qcDir = file.path("figures", "preprocessingMinfiEwasWater", "enmix"),
  preprocessingDir = file.path("figures", "preprocessingMinfiEwasWater", "qc"),
  postprocessingDir = file.path("figures", "preprocessingMinfiEwasWater", "metrics"),
  svaDir = file.path("figures", "svaEnmix"),
  glmDir = file.path("figures", "methylationGLM"),
  lmeDir = file.path("figures", "methylationLME"),
  figDir = file.path(outputDir, "assets", "figures"),
  verbose = FALSE,
  logs = FALSE,
  logDir = outputDir
)
}
\arguments{
\item{outputDir}{Character. Directory where the report project is written.}

\item{qcDir}{Character. Directory containing ENmix quality-control figures.}

\item{preprocessingDir}{Character. Directory containing preprocessing
quality-control figures.}

\item{postprocessingDir}{Character. Directory containing postprocessing
metric
figures.}

\item{svaDir}{Character. Directory containing SVA or batch-effect figures.}

\item{glmDir}{Character. Directory containing GLM figures.}

\item{lmeDir}{Character. Directory containing LME figures.}

\item{figDir}{Character. Directory used for generated report figure assets.}

\item{verbose}{Logical. If \code{TRUE}, emit progress messages with \code{message()}.}

\item{logs}{Logical. If \code{TRUE}, write progress messages to
\code{file.path(logDir, 'log_dnamReport.txt')}.}

\item{logDir}{Character. Directory for optional log files.}
}
\value{
A list with class \code{'dnaEPICO_dnamReport_prepared'}.
}
\description{
Prepare inputs for a DNA methylation report
}
\examples{
report_root <- file.path(tempdir(), "dnaepico-report-inputs")
prepared <- prepareDnamReportInputs(
    outputDir = file.path(report_root, "reports"),
    qcDir = file.path(
        report_root,
        "figures",
        "preprocessingMinfiEwasWater",
        "enmix"
    ),
    preprocessingDir = file.path(
        report_root,
        "figures",
        "preprocessingMinfiEwasWater",
        "qc"
    ),
    postprocessingDir = file.path(
        report_root,
        "figures",
        "preprocessingMinfiEwasWater",
        "metrics"
    ),
    svaDir = file.path(report_root, "figures", "svaEnmix")
)
inherits(prepared, "dnaEPICO_dnamReport_prepared")

}
