Plot raw and normalized methylation distributions — plotNormalizationMinfiEwasWater • dnaEPICO

Draw the density comparison plot used to inspect raw versus normalized data.

plotNormalizationMinfiEwasWater(
  RGSet,
  normData,
  targets,
  sexColumn = "Sex",
  display = FALSE,
  file = NULL,
  width = 2000L,
  height = 1000L,
  res = 150L,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_plotNormalizationMinfiEwasWater.txt"
)

Arguments

RGSet: An RGChannelSet aligned with targets.
normData: Object returned by normalizeMinfiEwasWater().
targets: Filtered phenotype data aligned with RGSet.
sexColumn: Character. Name of the phenotype column used to colour the density curves.
display: Logical. If TRUE, draw the plot on the active graphics device.
file: Character or NULL. TIFF file written when supplied.
width: Integer. TIFF width in pixels when file is supplied.
height: Integer. TIFF height in pixels when file is supplied.
res: Integer. TIFF resolution in DPI when file is supplied.
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

Invisibly returns the saved TIFF path when file is supplied, otherwise NULL.

Examples

ex <- dnaEPICO:::exampleMinfiMetricsStateDnaEpico()
plotNormalizationMinfiEwasWater(
  RGSet = ex$beta,
  normData = ex$normData,
  targets = ex$targets,
  sexColumn = "Sex",
  display = FALSE,
  verbose = FALSE,
  logs = FALSE
)