Write legacy preprocessingPheno outputs to disk — writePreprocessingPhenoOutputs • dnaEPICO

Write the legacy CSV, ZIP, and .RData outputs produced by preprocessingPheno(). This helper keeps file writing separate from the in-memory preprocessing steps.

writePreprocessingPhenoOutputs(
  preprocessingData,
  outputPheno = "data/preprocessingPheno",
  outputRData = "rData/preprocessingPheno/metrics",
  outputRDataMerge = "rData/preprocessingPheno/mergeData",
  outputDir = "data/preprocessingPheno",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_writePreprocessingPhenoOutputs.txt"
)

Arguments

preprocessingData: Object returned by preprocessingPheno() or a list with the same components.
outputPheno: Character. Directory used for saved phenotype CSV files.
outputRData: Character. Directory used for saved metric .RData files.
outputRDataMerge: Character. Directory used for saved merged phenotype-plus-beta .RData files.
outputDir: Character. Directory used for the Clock Foundation export files.
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_paths" containing the paths written to disk.

Examples

ex <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()
output_paths <- writePreprocessingPhenoOutputs(
  preprocessingData = ex$preprocessingData,
  outputPheno = file.path(ex$tempDir, "pheno"),
  outputRData = file.path(ex$tempDir, "metrics"),
  outputRDataMerge = file.path(ex$tempDir, "merge"),
  outputDir = file.path(ex$tempDir, "clock"),
  verbose = FALSE,
  logs = FALSE
)
names(output_paths)
#> [1] "timepoints"        "combinedPheno"     "combinedPhenoBeta"
#> [4] "betaCSV"           "betaZIP"           "phenoCF"