Generate a DNA methylation dashboard report

dnamReport(
  outputDir = "reports",
  phenoTab = NULL,
  enmixTab = file.path("figures", "preprocessingMinfiEwasWater", "enmix"),
  qcTab = file.path("figures", "preprocessingMinfiEwasWater", "qc"),
  svaTab = file.path("figures", "svaEnmix"),
  metricTab = file.path("figures", "preprocessingMinfiEwasWater", "metrics"),
  glmTab = NULL,
  lmerTab = NULL,
  logTab = outputDir,
  verbose = FALSE,
  logs = FALSE,
  projectName = "dnaEPICO",
  detPPath = NULL,
  detPThreshold = 0.01,
  cpgDetectionPath = NULL,
  sampleDetectionPath = NULL,
  logoPath = system.file("extdata", "dnaEPICO.svg", package = "dnaEPICO"),
  imagePattern = "\\.(png|jpg|jpeg|gif|webp|svg|tif|tiff)$",
  recursive = TRUE
)

Arguments

outputDir: Character. Directory where the Quarto project is written.
phenoTab: Character or NULL. CSV file shown in the Data tab. When NULL, the path is inferred from the Makefile output layout.
enmixTab: Character. Directory containing ENmix quality-control figures.
qcTab: Character. Directory containing Quality Control figures.
svaTab: Character. Directory containing Batch Effect or SVA figures.
metricTab: Character. Directory containing Metrics figures.
glmTab: Character or NULL. CSV file shown in the GLM Analysis tab. When NULL, the path is inferred from the Makefile output layout.
lmerTab: Character or NULL. CSV file shown in the LMER Analysis tab. When NULL, the path is inferred from the Makefile output layout.
logTab: Character. Directory containing workflow logs shown in the Logs tab.
verbose: Logical. If TRUE, emit progress messages.
logs: Logical. If TRUE, write a report log.
projectName: Character. Name used for the generated Quarto project.
detPPath: Character or NULL. RData file containing the detection P-value matrix object detP, used to build the quality-control tables. When NULL, the path is inferred from the Makefile output layout.
detPThreshold: Numeric. Detection P-value threshold used when summarising the detP matrix.
cpgDetectionPath: Character or NULL. Optional fallback CpG detection summary CSV.
sampleDetectionPath: Character or NULL. Optional fallback sample detection summary CSV.
logoPath: Character. Path to the navbar logo. Defaults to the packaged inst/extdata/dnaEPICO.svg asset.
imagePattern: Character. Regular expression used to identify image files inside the section directories.
recursive: Logical. If TRUE, search section directories recursively.

Value

A list with class "dnaEPICO_dnamReport".

Examples

report_root <- file.path(tempdir(), "dnaepico-dnam-report")
pheno_file <- file.path(
  report_root,
  "data",
  "model1",
  "preprocessingMinfiEwasWater",
  "phenoLC.csv"
)
dir.create(dirname(pheno_file), recursive = TRUE, showWarnings = FALSE)
utils::write.csv(
  data.frame(
    UID = c("sample1", "sample2"),
    Timepoint = c(1, 2),
    Sex = c("F", "M")
  ),
  pheno_file,
  row.names = FALSE
)

result <- dnamReport(
  outputDir = file.path(report_root, "reports", "model1"),
  phenoTab = pheno_file,
  enmixTab = file.path(
    report_root,
    "figures",
    "model1",
    "preprocessingMinfiEwasWater",
    "enmix"
  ),
  qcTab = file.path(
    report_root,
    "figures",
    "model1",
    "preprocessingMinfiEwasWater",
    "qc"
  ),
  svaTab = file.path(report_root, "figures", "model1", "svaEnmix"),
  metricTab = file.path(
    report_root,
    "figures",
    "model1",
    "preprocessingMinfiEwasWater",
    "metrics"
  ),
  logTab = file.path(report_root, "logs", "model1")
)
result$status
#> [1] "rendered"