Build raw minfi preprocessing objects

Create a raw MethylSet, RatioSet, and genome-mapped object from an RGChannelSet, and return them together in a single structured object.

buildRawMinfiEwasWater(
  RGSet,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_buildRawMinfiEwasWater.txt"
)

Arguments

RGSet

An RGChannelSet.

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_minfiEwasWater_raw" containing MSet, RatioSet, and GSet.

Examples

ex <- dnaEPICO:::exampleMinfiBaseDataDnaEpico()
raw_data <- buildRawMinfiEwasWater(
  RGSet = ex$RGSet,
  verbose = FALSE,
  logs = FALSE
)
names(raw_data)
#> [1] "MSet"     "RatioSet" "GSet"