Summarize CpG-wise Gaussian GLM results for one-timepoint analyses — summarizeMethylationGLMModels • dnaEPICO

Return phenotype-specific CpG coefficient tables from the compact fit-time results produced by fitMethylationGLMModels().

summarizeMethylationGLMModels(
  modelResults,
  preparedData,
  summaryResidualSD = TRUE,
  summaryPval = NA,
  padjmethod = "fdr",
  nCores = 1L,
  libPath = NULL,
  glmLibs = "glm2",
  chunkSize = NULL,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationGLM.txt"
)

Arguments

modelResults: Object returned by fitMethylationGLMModels().
preparedData: Object returned by prepareMethylationGLMData().
summaryResidualSD: Logical. If TRUE, add residual standard deviations to each CpG summary row.
summaryPval: Numeric or NA. Optional p-value filter applied to the returned summary tables. NA keeps all rows.
padjmethod: Character. Adjustment method passed to stats::p.adjust() for omnibus p-values across CpGs within each phenotype and tested term.
nCores: Integer. Number of worker processes to use while extracting summary rows.
libPath: Character vector or NULL. Optional library paths forwarded to worker processes.
glmLibs: Character vector or comma-separated string of package names to check on worker processes. The default is 'glm2'.
chunkSize: Integer or NULL. Number of CpGs to process per parallel chunk. NULL chooses a value automatically.
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_summaries' containing the optionally filtered summary tables in summaries and the complete CpG-level tables in diagnosticSummaries. Diagnostics, annotation, and report output use the complete tables so summaryPval does not remove CpGs from those outputs. modelMessages retains native messages, warnings, and errors for every attempted CpG.

Examples

ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
summary_results <- summarizeMethylationGLMModels(
  modelResults = ex$modelResults,
  preparedData = ex$preparedData,
  summaryResidualSD = TRUE,
  summaryPval = NA,
  nCores = 1,
  verbose = FALSE,
  logs = FALSE
)
names(summary_results$summaries)
#> [1] "status"