Annotate one-timepoint GLM summary tables with array annotation metadata — annotateMethylationGLMSummaries • dnaEPICO

Merge phenotype-specific CpG summary tables with probe annotation metadata and return a single annotated result table.

annotateMethylationGLMSummaries(
  modelSummaries,
  annotationObject,
  annotationCols = c("Name", "chr", "pos", "UCSC_RefGene_Group", "UCSC_RefGene_Name",
    "Relation_to_Island", "GencodeV41_Group"),
  gencodeHub = FALSE,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationGLM.txt"
)

Arguments

modelSummaries: Object returned by summarizeMethylationGLMModels() or a named list of CpG summary data frames.
annotationObject: Character package/object name, annotation data frame, or annotation object understood by minfi::getAnnotation().
annotationCols: Character vector or comma-separated string of annotation columns to append.
gencodeHub: Logical. If TRUE, retrieve the package-managed GENCODE gene resource from AnnotationHub and append direct gene-body and nearest transcription-start-site annotations. This requires GRCh38 coordinates.
verbose: Logical. If TRUE, emit progress messages with message().
logs: Logical. If TRUE, write the same messages to a log file.
log_dir: Character or NULL. Directory used for the log file when logs = TRUE.
log_file: Character. File name used when logs = TRUE.

Value

A list with class 'dnaEPICO_methylationGLM_annotation' containing the annotated summary table and any requested annotation columns that were unavailable in the chosen annotation object.

Examples

ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
annotation_data <- annotateMethylationGLMSummaries(
  modelSummaries = ex$modelSummaries,
  annotationObject = ex$annotationData,
  annotationCols = "Name,chr,pos",
  verbose = FALSE,
  logs = FALSE
)
names(annotation_data)
#> [1] "data"                  "fitFailures"           "modelMessages"        
#> [4] "annotationColumnsUsed" "missingAnnotationCols" "gencodeHub"