Collect significant CpG coefficient tables from fitted one-timepoint GLMs — collectSignificantCpGsMethylationGLM • dnaEPICO

Collect coefficient tables for CpGs selected by the configured target test. Selection uses target-term omnibus p-values when omnibus testing was enabled during fitting, and phenotype main-effect or interaction coefficient p-values otherwise.

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

Arguments

modelResults: Object returned by fitMethylationGLMModels().
pvalThreshold: Numeric. Threshold applied to omnibus p-values when omnibus testing was enabled during model fitting, or to phenotype main-effect or interaction coefficient p-values otherwise.
interactionTerm: Character or NULL. Optional interaction term.
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_significant_cpgs'.

Examples

ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
significant_cpgs <- collectSignificantCpGsMethylationGLM(
  modelResults = ex$modelResults,
  pvalThreshold = 1,
  verbose = FALSE,
  logs = FALSE
)
names(significant_cpgs)
#> [1] "status"