Summarize CpG-wise mixed-effects model fits for longitudinal analyses — summarizeMethylationLMEModels • dnaEPICO

Extract phenotype-specific fixed-effect tables from the fitted mixed-effects model object returned by fitMethylationLMEModels().

summarizeMethylationLMEModels(
  modelResults,
  preparedData,
  summaryPval = NA,
  nCores = 1L,
  chunkSize = NULL,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationLME.txt"
)

Arguments

modelResults: Object returned by fitMethylationLMEModels().
preparedData: Object returned by prepareMethylationLMEData().
summaryPval: Numeric or NA. Optional p-value filter applied to the returned summary tables. NA keeps all rows.
nCores: Integer. Number of worker processes to use while extracting summary rows.
chunkSize: Integer or NULL. Number of CpGs processed 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_methylationLME_summaries" containing one CpG-level summary data frame per phenotype.

Examples

ex <- dnaEPICO:::exampleMethylationLMEStateDnaEpico()
summary_results <- summarizeMethylationLMEModels(
  modelResults = ex$modelResults,
  preparedData = ex$preparedData,
  summaryPval = NA,
  nCores = 1,
  verbose = FALSE,
  logs = FALSE
)
names(summary_results$summaries)
#> [1] "score"