% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/methylationGLM_steps.R
\name{annotateMethylationGLMSummaries}
\alias{annotateMethylationGLMSummaries}
\title{Annotate one-timepoint GLM summary tables with array annotation metadata}
\usage{
annotateMethylationGLMSummaries(
  modelSummaries,
  annotationObject,
  annotationCols = c("Name", "chr", "pos", "UCSC_RefGene_Group", "UCSC_RefGene_Name",
    "Relation_to_Island", "GencodeV41_Group"),
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationGLM.txt"
)
}
\arguments{
\item{modelSummaries}{Object returned by \code{summarizeMethylationGLMModels()}
or a named list of CpG summary data frames.}

\item{annotationObject}{Character package/object name, annotation data frame,
or annotation object understood by \code{minfi::getAnnotation()}.}

\item{annotationCols}{Character vector or comma-separated string of
annotation
columns to append.}

\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_methylationGLM_annotation'}
containing the annotated summary table and any requested annotation columns
that were unavailable in the chosen annotation object.
}
\description{
Merge phenotype-specific CpG summary tables with probe annotation metadata
and
return a single annotated result table.
}
\examples{
ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
annotation_data <- annotateMethylationGLMSummaries(
    modelSummaries = ex$modelSummaries,
    annotationObject = ex$annotationData,
    annotationCols = "Name,chr,pos",
    verbose = FALSE,
    logs = FALSE
)
names(annotation_data)

}
