% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocessingPheno_steps.R
\name{writePreprocessingPhenoOutputs}
\alias{writePreprocessingPhenoOutputs}
\title{Write preprocessingPheno outputs to disk}
\usage{
writePreprocessingPhenoOutputs(
  preprocessingData,
  outputPheno = "data/preprocessingPheno",
  outputRData = "rData/preprocessingPheno/metrics",
  outputRDataMerge = "rData/preprocessingPheno/mergeData",
  outputDir = "data/preprocessingPheno",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_writePreprocessingPhenoOutputs.txt"
)
}
\arguments{
\item{preprocessingData}{Object returned by \code{preprocessingPheno()} or a list
with the same components.}

\item{outputPheno}{Character. Directory used for saved phenotype CSV files.}

\item{outputRData}{Character. Directory used for saved metric \code{.RData} files.}

\item{outputRDataMerge}{Character. Directory used for saved merged
phenotype-plus-beta \code{.RData} files.}

\item{outputDir}{Character. Directory used for the Clock Foundation export
files.}

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

\item{logs}{Logical. If \code{TRUE}, write the same messages to a log file.}

\item{log_dir}{Character or \code{NULL}. Directory used for the log file when
\code{logs = TRUE}.}

\item{log_file}{Character. File name used when \code{logs = TRUE}.}
}
\value{
A list with class \code{'dnaEPICO_preprocessingPheno_paths'}
containing the paths written to disk.
}
\description{
Write the CSV, ZIP, and \code{.RData} outputs produced by
\code{preprocessingPheno()}. This helper keeps file writing separate from the
in-memory preprocessing steps.
}
\examples{
ex <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()
output_paths <- writePreprocessingPhenoOutputs(
    preprocessingData = ex$preprocessingData,
    outputPheno = file.path(ex$tempDir, "pheno"),
    outputRData = file.path(ex$tempDir, "metrics"),
    outputRDataMerge = file.path(ex$tempDir, "merge"),
    outputDir = file.path(ex$tempDir, "clock"),
    verbose = FALSE,
    logs = FALSE
)
names(output_paths)

}
