Prepare inputs for a DNA methylation report

prepareDnamReportInputs(
  outputDir = "reports",
  qcDir = file.path("figures", "preprocessingMinfiEwasWater", "enmix"),
  preprocessingDir = file.path("figures", "preprocessingMinfiEwasWater", "qc"),
  postprocessingDir = file.path("figures", "preprocessingMinfiEwasWater", "metrics"),
  svaDir = file.path("figures", "svaEnmix"),
  glmDir = file.path("figures", "methylationGLM_T1"),
  glmmDir = file.path("figures", "methylationGLMM_T1T2"),
  figDir = file.path(outputDir, "assets", "figures"),
  verbose = FALSE,
  logs = FALSE,
  logDir = outputDir
)

Arguments

outputDir: Character. Directory where the report project is written.
qcDir: Character. Directory containing ENmix quality-control figures.
preprocessingDir: Character. Directory containing preprocessing quality-control figures.
postprocessingDir: Character. Directory containing postprocessing metric figures.
svaDir: Character. Directory containing SVA or batch-effect figures.
glmDir: Character. Directory containing GLM figures.
glmmDir: Character. Directory containing GLMM figures.
figDir: Character. Directory used for generated report figure assets.
verbose: Logical. If TRUE, emit progress messages with message().
logs: Logical. If TRUE, write progress messages to file.path(logDir, "log_dnamReport.txt").
logDir: Character. Directory for optional log files.

Value

A list with class "dnaEPICO_dnamReport_prepared".

Examples

report_root <- file.path(tempdir(), "dnaepico-report-inputs")
prepared <- prepareDnamReportInputs(
  outputDir = file.path(report_root, "reports"),
  qcDir = file.path(
    report_root,
    "figures",
    "preprocessingMinfiEwasWater",
    "enmix"
  ),
  preprocessingDir = file.path(
    report_root,
    "figures",
    "preprocessingMinfiEwasWater",
    "qc"
  ),
  postprocessingDir = file.path(
    report_root,
    "figures",
    "preprocessingMinfiEwasWater",
    "metrics"
  ),
  svaDir = file.path(report_root, "figures", "svaEnmix")
)
inherits(prepared, "dnaEPICO_dnamReport_prepared")
#> [1] TRUE