Collect significant longitudinal model terms from fitted mixed-effects models — collectSignificantInteractionsMethylationLME • dnaEPICO

Collect raw coefficient tables for CpGs whose phenotype main effect or requested interaction p-value passes the chosen threshold.

collectSignificantInteractionsMethylationLME(
  modelResults,
  pvalThreshold = 0.05,
  interactionTerm = NULL,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationLME.txt"
)

Arguments

modelResults: Object returned by fitMethylationLMEModels().
pvalThreshold: Numeric. Threshold applied to the extracted phenotype or interaction p-values.
interactionTerm: Character or NULL. Optional interaction term. When NULL, phenotype main effects are used.
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_significant" containing the retained coefficient tables for each phenotype.

Examples

ex <- dnaEPICO:::exampleMethylationLMEStateDnaEpico()
significant_hits <- collectSignificantInteractionsMethylationLME(
  modelResults = ex$modelResults,
  pvalThreshold = 1,
  verbose = FALSE,
  logs = FALSE
)
names(significant_hits)
#> [1] "score"