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

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

collectSignificantCpGsMethylationGLM_T1(
  modelResults,
  pvalThreshold = 0.05,
  interactionTerm = NULL,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationGLM_T1.txt"
)

Arguments

modelResults: Object returned by fitMethylationGLM_T1Models().
pvalThreshold: Numeric. Threshold applied to phenotype main-effect or interaction p-values.
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_T1_significant_cpgs".

Examples

ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
significant_cpgs <- collectSignificantCpGsMethylationGLM_T1(
  modelResults = ex$modelResults,
  pvalThreshold = 1,
  verbose = FALSE,
  logs = FALSE
)
names(significant_cpgs)
#> [1] "status"