Combine selected timepoints for downstream longitudinal modeling

Source: R/preprocessingPheno_steps.R

Combine selected timepoints that were already aligned by splitTimepointsPreprocessingPheno() into the wide phenotype-plus-beta objects used by downstream longitudinal models.

combineTimepointsPreprocessingPheno(
  timepointData,
  combineTimepoints = "1,2",
  methylationScale = "beta",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_combineTimepointsPreprocessingPheno.txt"
)

Arguments

timepointData

Object returned by splitTimepointsPreprocessingPheno().

combineTimepoints

Character vector or comma-separated string of timepoints to combine.

methylationScale

Character. Methylation metric used in 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_combined" containing the combined phenotype table, merged phenotype-plus-beta table, selected timepoints, and output suffix.

Examples

ex <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()
combined_data <- combineTimepointsPreprocessingPheno(
  timepointData = ex$timepointData,
  combineTimepoints = "1,2",
  verbose = FALSE,
  logs = FALSE
)
combined_data$suffix
#> [1] "T1T2"