Load methylation metric matrices for preprocessingPheno — loadMetricsPreprocessingPheno • dnaEPICO

Load the metric matrices generated by preprocessingMinfiEwasWater() and return them as a single in-memory object for downstream phenotype alignment.

loadMetricsPreprocessingPheno(
  betaPath,
  mPath,
  cnPath,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_loadMetricsPreprocessingPheno.txt"
)

Arguments

betaPath: Character. Path to the saved beta-value object.
mPath: Character. Path to the saved M-value object.
cnPath: Character. Path to the saved copy-number object.
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_preprocessingPheno_metrics' containing beta, m, and cn.

Examples

ex <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()
metrics_data <- loadMetricsPreprocessingPheno(
  betaPath = ex$betaPath,
  mPath = ex$mPath,
  cnPath = ex$cnPath,
  verbose = FALSE,
  logs = FALSE
)
names(metrics_data)
#> [1] "beta"              "m"                 "cn"               
#> [4] "methylationRanges"