Build Clock Foundation input tables from preprocessingPheno data — buildClockFoundationInputsPreprocessingPheno • dnaEPICO

Prepare the beta and phenotype tables commonly exported for Clock Foundation style downstream workflows, without writing them to disk.

buildClockFoundationInputsPreprocessingPheno(
  beta,
  pheno,
  SampleID = "Sample_Name",
  sexColumn = "Sex",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_buildClockFoundationInputsPreprocessingPheno.txt"
)

Arguments

beta: Numeric matrix of beta values with probes in rows and samples in columns.
pheno: Phenotype data frame aligned with the beta matrix columns.
SampleID: Character. Name of the phenotype sample identifier column.
sexColumn: Character. Name of the phenotype sex column.
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_clock" containing betaCSV and phenoCF.

Examples

ex <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()
clock_inputs <- buildClockFoundationInputsPreprocessingPheno(
  beta = ex$timepointData$data[["1"]]$beta,
  pheno = ex$timepointData$data[["1"]]$pheno,
  SampleID = "Sample_Name",
  sexColumn = "Sex",
  verbose = FALSE,
  logs = FALSE
)
names(clock_inputs)
#> [1] "betaCSV" "phenoCF"