Write svaEnmix outputs to disk — writeSvaEnmixOutputs • dnaEPICO

Write the legacy CSV, .RData, and text-summary outputs used by the original svaEnmix() workflow.

writeSvaEnmixOutputs(
  svaData,
  mergedPheno,
  analysisData = NULL,
  phenoFile = NULL,
  dataBaseDir = "data",
  rBaseDir = "rData",
  scriptLabel = "svaEnmix",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_writeSvaEnmixOutputs.txt"
)

Arguments

svaData: Object returned by estimateSvaEnmixControls().
mergedPheno: Phenotype data frame returned by mergeSvaTargetsEnmix().
analysisData: Optional object returned by analyzeSvaEnmix().
phenoFile: Character or NULL. When supplied, mergedPheno is written back to this path for legacy compatibility.
dataBaseDir: Character. Base directory used for saved data outputs.
rBaseDir: Character. Base directory used for saved .RData outputs.
scriptLabel: Character. Label used to create the output subdirectory.
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_svaEnmix_paths" containing the paths written to disk.

Examples

ex <- dnaEPICO:::exampleSvaAnalysisStateDnaEpico()
temp_dir <- tempdir()
output_paths <- writeSvaEnmixOutputs(
  svaData = list(sva = ex$sva),
  mergedPheno = ex$mergedPheno,
  analysisData = ex$analysisData,
  phenoFile = file.path(temp_dir, "phenoLC.csv"),
  dataBaseDir = file.path(temp_dir, "data"),
  rBaseDir = file.path(temp_dir, "rData"),
  scriptLabel = "svaEnmixExample",
  verbose = FALSE,
  logs = FALSE
)
names(output_paths)
#> [1] "svaRData"     "svaCSV"       "phenoWithSva" "dataDir"      "rDir"