Split phenotype and methylation data by timepoint — splitTimepointsPreprocessingPheno • dnaEPICO

Align phenotype rows and metric matrices for each requested timepoint, and precompute the per-timepoint phenotype-plus-beta objects used by downstream modeling functions.

splitTimepointsPreprocessingPheno(
  pheno,
  metricsData,
  SampleID = "Sample_Name",
  timeVar = "Timepoint",
  timepoints = "1,2",
  methylationScale = "beta",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_splitTimepointsPreprocessingPheno.txt"
)

Arguments

pheno: Data frame containing phenotype information.
metricsData: Object returned by loadMetricsPreprocessingPheno().
SampleID: Character. Name of the sample identifier column in pheno.
timeVar: Character. Name of the timepoint column in pheno.
timepoints: Character vector or comma-separated string of timepoints to retain.
methylationScale: Character. Methylation metric to use for the merged modeling table. One of "beta", "m", or "cn".
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_timepoints" containing the parsed timepoints and aligned per-timepoint subsets.

Examples

ex <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()
timepoint_data <- splitTimepointsPreprocessingPheno(
  pheno = ex$pheno,
  metricsData = ex$metricsData,
  SampleID = "Sample_Name",
  timeVar = "Timepoint",
  timepoints = "1,2",
  verbose = FALSE,
  logs = FALSE
)
timepoint_data$timepoints
#> [1] "1" "2"