% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocessingMinfiEwasWater_steps.R
\name{normalizeMinfiEwasWater}
\alias{normalizeMinfiEwasWater}
\title{Normalize filtered samples with minfi and wateRmelon methods}
\usage{
normalizeMinfiEwasWater(
  sampleData,
  sexColumn = "Sex",
  normMethods = "adjustedfunnorm",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_normalizeMinfiEwasWater.txt"
)
}
\arguments{
\item{sampleData}{Object returned by \code{filterSamplesMinfiEwasWater()}.}

\item{sexColumn}{Character. Name of the phenotype column used as the optional
sex covariate for normalization methods that support it.}

\item{normMethods}{Character vector or semicolon-separated string of
normalization methods. Supported values are \code{'adjustedfunnorm'},
\code{'funnorm'}, \code{'illumina'}, \code{'quantile'}, and \code{'swan'}.}

\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_norm'} containing the
requested normalized objects and the first method as \code{primary}.
}
\description{
Apply one or more supported normalization methods to a filtered \code{RGSet} and
return all normalized objects together in a single result object.
}
\examples{
\dontshow{if (requireNamespace("minfiData", quietly = TRUE)) withAutoprint(\{ # examplesIf}
ex <- dnaEPICO:::exampleMinfiBaseDataDnaEpico()
sample_data <- filterSamplesMinfiEwasWater(
    RGSet = ex$RGSet,
    targets = ex$targets,
    failedSamples = character(0),
    SampleID = "Sample_Name",
    verbose = FALSE,
    logs = FALSE
)
norm_data <- normalizeMinfiEwasWater(
    sampleData = sample_data,
    sexColumn = "Sex",
    normMethods = "quantile",
    verbose = FALSE,
    logs = FALSE
)
names(norm_data$normalized)
\dontshow{\}) # examplesIf}
}
