Fit CpG-wise Gaussian GLMs for one-timepoint methylation analyses — fitMethylationGLM

Fit one Gaussian GLM per CpG for each phenotype requested in the object returned by prepareMethylationGLM_T1Data().

fitMethylationGLM_T1Models(
  preparedData,
  nCores = 1L,
  libPath = NULL,
  glmLibs = "glm2",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationGLM_T1.txt"
)

Arguments

preparedData: Object returned by prepareMethylationGLM_T1Data().
nCores: Integer. Number of worker processes to use.
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".
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_models" containing fitted model lists, model formulas, and counts of failed CpG fits.

Examples

ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
model_results <- fitMethylationGLM_T1Models(
  preparedData = ex$preparedData,
  nCores = 1,
  verbose = FALSE,
  logs = FALSE
)
names(model_results$fits)
#> [1] "status"