## ----setup, include = FALSE---------------------------------------------------
startTime <- Sys.time()
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    crop = NULL,
    message = FALSE,
    warning = FALSE
)

library(dnaEPICO)

can_run_preprocessing <- requireNamespace("minfiData", quietly = TRUE) &&
    requireNamespace("IlluminaHumanMethylation450kmanifest", quietly = TRUE) &&
    requireNamespace(
        "IlluminaHumanMethylation450kanno.ilmn12.hg19",
        quietly = TRUE
    )

can_run_sva <- requireNamespace("minfiData", quietly = TRUE)

## ----install-dnaepico, eval = FALSE-------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE)) {
#     install.packages("BiocManager")
# }
# 
# BiocManager::install("paulYRP/dnaEPICO")
# 
# BiocManager::valid()

## ----load-dnaepico, eval = FALSE, message = FALSE-----------------------------
# library("dnaEPICO")

## ----preprocessing-local-inputs, eval = can_run_preprocessing-----------------
preprocessing_inputs <- dnaEPICO:::exampleMinfiIdatInputsDnaEpico(n = 6L)

names(preprocessing_inputs)
preprocessing_inputs$tempDir
basename(preprocessing_inputs$phenoFile)
head(
    basename(list.files(
        preprocessing_inputs$idatFolder,
        full.names = TRUE
    )),
    4
)
basename(preprocessing_inputs$probeExclusionPath)

## ----preprocessing-local, eval = can_run_preprocessing------------------------
preprocessResult <- preprocessingMinfiEwasWater(
    phenoFile = preprocessing_inputs$phenoFile,
    idatFolder = preprocessing_inputs$idatFolder,
    outputLogs = file.path(preprocessing_inputs$tempDir, "logs"),
    nSamples = 6,
    SampleID = "Sample_Name",
    arrayType = preprocessing_inputs$arrayType,
    annotationVersion = preprocessing_inputs$annotationVersion,
    scriptLabel = "preprocessingMinfiEwasWater",
    baseDataFolder = file.path(preprocessing_inputs$tempDir, "rData"),
    figureBaseDir = file.path(preprocessing_inputs$tempDir, "figures"),
    detPThreshold = 1,
    normMethods = "quantile",
    sexColumn = "Sex",
    removeSexMismatch = FALSE,
    pvalThreshold = 1,
    chrToRemove = "",
    snpsToRemove = "SBE",
    mafThreshold = 1,
    probeExclusionPath = preprocessing_inputs$probeExclusionPath,
    plotGroupVar = "Sex",
    lcRef = "saliva",
    phenoOrder = "Sample_Name;Sex;Basename;Sentrix_ID;Sentrix_Position",
    lcPhenoDir = preprocessing_inputs$tempDir,
    display = FALSE,
    verbose = FALSE,
    logs = FALSE,
    saveOutputs = FALSE
)

class(preprocessResult)
names(preprocessResult)
head(preprocessResult$targets[, c(
    "Sample_Name",
    "Sex",
    "Sentrix_ID",
    "Sentrix_Position"
)])

## ----preprocessing-local-inspect, eval = can_run_preprocessing----------------
class(preprocessResult$RGSet)
names(preprocessResult$metricsData)
head(preprocessResult$lcData$phenoLC[, 1:6])

## ----sva-local-inputs, eval = can_run_sva, message = FALSE, warning = FALSE----
sva_inputs <- dnaEPICO:::exampleMinfiBaseDataDnaEpico()
sva_temp_dir <- tempdir()
sva_targets_file <- file.path(sva_temp_dir, "sva_targets.csv")
sva_rgset_file <- file.path(sva_temp_dir, "sva_RGSet.RData")

names(sva_inputs)
class(sva_inputs$RGSet)
utils::write.csv(sva_inputs$targets, sva_targets_file, row.names = FALSE)
RGSet <- sva_inputs$RGSet
save(RGSet, file = sva_rgset_file)

basename(c(sva_targets_file, sva_rgset_file))
file.exists(c(sva_targets_file, sva_rgset_file))

## ----sva-local, eval = can_run_sva, message = FALSE, warning = FALSE----------
svaResult <- svaEnmix(
    phenoFile = sva_targets_file,
    rgsetData = sva_rgset_file,
    outputLogs = file.path(tempdir(), "logs"),
    SampleID = "Sample_Name",
    arrayType = "IlluminaHumanMethylation450k",
    annotationVersion = "ilmn12.hg19",
    SentrixIDColumn = "Sentrix_ID",
    SentrixPositionColumn = "Sentrix_Position",
    ctrlSvaPercVar = 0.90,
    ctrlSvaFlag = 1,
    scriptLabel = "svaEnmix",
    display = FALSE,
    verbose = FALSE,
    logs = FALSE,
    saveOutputs = FALSE
)

class(svaResult)
names(svaResult)
dim(svaResult$svaData$sva)
head(svaResult$mergedPheno[, 1:min(6, ncol(svaResult$mergedPheno))])

## ----sva-local-inspect, eval = can_run_sva, message = FALSE, warning = FALSE----
class(svaResult$analysisData)
names(svaResult$analysisData)

## ----preprocessingPheno-local-inputs, message = FALSE, warning = FALSE--------
pheno_inputs <- dnaEPICO:::examplePreprocessingPhenoStateDnaEpico()

names(pheno_inputs)
pheno_inputs$tempDir
basename(c(
    pheno_inputs$phenoPath,
    pheno_inputs$betaPath,
    pheno_inputs$mPath,
    pheno_inputs$cnPath
))

## ----preprocessingPheno-local, message = FALSE, warning = FALSE---------------
phenoResult <- preprocessingPheno(
    phenoFile = pheno_inputs$phenoPath,
    betaPath = pheno_inputs$betaPath,
    mPath = pheno_inputs$mPath,
    cnPath = pheno_inputs$cnPath,
    SampleID = "Sample_Name",
    timeVar = "Timepoint",
    timepoints = "1,2",
    combineTimepoints = "1,2",
    outputPheno = file.path(pheno_inputs$tempDir, "data", "preprocessingPheno"),
    outputRData = file.path(
        pheno_inputs$tempDir,
        "rData",
        "preprocessingPheno",
        "metrics"
    ),
    outputRDataMerge = file.path(
        pheno_inputs$tempDir,
        "rData",
        "preprocessingPheno",
        "mergeData"
    ),
    sexColumn = "Sex",
    outputLogs = file.path(pheno_inputs$tempDir, "logs"),
    outputDir = file.path(pheno_inputs$tempDir, "clockFoundation"),
    verbose = FALSE,
    logs = FALSE,
    saveOutputs = FALSE
)

class(phenoResult)
names(phenoResult)
names(phenoResult$combinedData)
head(phenoResult$combinedData$phenoMethylation[, 1:6])

## ----preprocessingPheno-local-inspect, message = FALSE, warning = FALSE-------
names(phenoResult$clockFoundation)
head(phenoResult$clockFoundation$phenoCF)

## ----vignette-date, echo = FALSE----------------------------------------------
Sys.time()

## ----vignette-wallclock, echo = FALSE-----------------------------------------
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits = 3)

## ----vignette-session-info, echo = FALSE--------------------------------------
sessionInfo()