% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocessingPheno_steps.R
\name{buildClockFoundationInputsPreprocessingPheno}
\alias{buildClockFoundationInputsPreprocessingPheno}
\title{Build Clock Foundation input tables from preprocessingPheno data}
\usage{
buildClockFoundationInputsPreprocessingPheno(
  beta,
  pheno,
  SampleID = "Sample_Name",
  sexColumn = "Sex",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_buildClockFoundationInputsPreprocessingPheno.txt"
)
}
\arguments{
\item{beta}{Numeric matrix of beta values with probes in rows and samples in
columns.}

\item{pheno}{Phenotype data frame aligned with the beta matrix columns.}

\item{SampleID}{Character. Name of the phenotype sample identifier column.}

\item{sexColumn}{Character. Name of the phenotype sex column.}

\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_clock'}
containing \code{betaCSV} and \code{phenoCF}.
}
\description{
Prepare the beta and phenotype tables commonly exported for Clock Foundation
style downstream workflows, without writing them to disk.
}
\examples{
ex <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()
clock_inputs <- buildClockFoundationInputsPreprocessingPheno(
    beta = ex$timepointData$data[["1"]]$beta,
    pheno = ex$timepointData$data[["1"]]$pheno,
    SampleID = "Sample_Name",
    sexColumn = "Sex",
    verbose = FALSE,
    logs = FALSE
)
names(clock_inputs)

}
