% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocessingMinfiEwasWater_steps.R
\name{predictSexMinfiEwasWater}
\alias{predictSexMinfiEwasWater}
\title{Predict biological sex from a filtered raw-data object}
\usage{
predictSexMinfiEwasWater(
  rawData,
  targets,
  SampleID = "Sample_Name",
  sexColumn = "Sex",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_predictSexMinfiEwasWater.txt"
)
}
\arguments{
\item{rawData}{Object returned by \code{buildRawMinfiEwasWater()}.}

\item{targets}{Filtered phenotype data frame aligned with \code{rawData}.}

\item{SampleID}{Character. Name of the sample identifier column in \code{targets}.}

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

\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_minfiEwasWater_sex'} containing the sex
prediction result, aligned phenotype data, plotting data, and mismatch
table.
}
\description{
Predict sample sex from a genome-mapped methylation object, align the
predictions with phenotype data, and return a structured object that can be
plotted or merged into downstream phenotype tables.
}
\examples{
\dontshow{if (requireNamespace("minfiData", quietly = TRUE)) withAutoprint(\{ # examplesIf}
ex <- dnaEPICO:::exampleMinfiWorkflowStateDnaEpico()
sex_data <- predictSexMinfiEwasWater(
    rawData = ex$rawFiltered,
    targets = ex$sampleData$targets,
    SampleID = "Sample_Name",
    sexColumn = "Sex",
    verbose = FALSE,
    logs = FALSE
)
names(sex_data)
\dontshow{\}) # examplesIf}
}
