% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocessingPheno_steps.R
\name{combineTimepointsPreprocessingPheno}
\alias{combineTimepointsPreprocessingPheno}
\title{Combine selected timepoints for downstream longitudinal modeling}
\usage{
combineTimepointsPreprocessingPheno(
  timepointData,
  combineTimepoints = "1,2",
  methylationScale = "beta",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_combineTimepointsPreprocessingPheno.txt"
)
}
\arguments{
\item{timepointData}{Object returned by
\code{splitTimepointsPreprocessingPheno()}.}

\item{combineTimepoints}{Character vector or comma-separated string of
timepoints to combine.}

\item{methylationScale}{Character. Methylation metric used in the merged
modeling table. One of \code{'Beta'}, \code{'M'}, or \code{'CN'}, case-insensitively.}

\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_combined'}
containing the combined phenotype table, merged phenotype-plus-beta table,
selected timepoints, and output suffix.
}
\description{
Combine selected timepoints that were already aligned by
\code{splitTimepointsPreprocessingPheno()} into the wide phenotype-plus-beta
objects used by downstream longitudinal models.
}
\examples{
ex <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()
combined_data <- combineTimepointsPreprocessingPheno(
    timepointData = ex$timepointData,
    combineTimepoints = "1,2",
    verbose = FALSE,
    logs = FALSE
)
combined_data$suffix

}
