## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------
BiocStyle::latex()

## ----minfiDatatargets, cache=TRUE, message=FALSE-------------------------
library(MethylAid)
library(minfiData)
baseDir <- system.file("extdata", package = "minfiData")
targets <- read.metharray.sheet(baseDir)

## ----minfiDataMethylAid, cache=TRUE, eval=FALSE--------------------------
## data <- summarize(targets)
## visualize(data)

## ----presummarized, message=FALSE, eval=FALSE----------------------------
## library(MethylAid)
## data(exampleData)
## visualize(exampleData)

## ----tcgatargets, eval=FALSE---------------------------------------------
## sdrfFile <- list.files(pattern="sdrf", full.name=TRUE)
## targets <- read.table(sdrfFile, header=TRUE, sep="\t")
## path <- "path_to_idat_files"
## targets <- targets[file.exists(file.path(path, targets$Array.Data.File)),]
## targets <- targets[grepl("Red", targets$Array.Data.File),]
## targets$Basename <- gsub("_Red.*$", "", file.path(path, targets$Array.Data.File))
## rownames(targets) <- basename(targets$Basename)
## head(targets)

## ----tcgaMethylAid, eval=FALSE-------------------------------------------
## summarize(targets, batchSize = 15, file = "tcgaBRCA")
## load("tcgaBRCA.RData")
## visualize(tcgaBRCA)

## ----geotargets, eval=FALSE, tidy=FALSE----------------------------------
## library(GEOquery)
## gse <- getGEO("GSE42861")
## targets <- pData(phenoData(gse[[1]]))
## path <- "path_to_idat_files"
## targets$Basename <- file.path(path,
## gsub("_Grn.*$", "", basename(targets$supplementary_file)))
## rownames(targets) <- basename(targets$Basename)

## ----geoMethylAid, eval=FALSE--------------------------------------------
## summarize(targets, batchSize = 15, file="RA")
## load("RA.RData")
## visualize(RA)

## ----tcgaMethylAidmc, eval=FALSE-----------------------------------------
## library(BiocParallel)
## tcga <- summarize(targets, batchSize = 15, BPPARAM = MulticoreParam(workers = 8))

## ----tcgaMethylAidsge, eval=FALSE, tidy=FALSE----------------------------
## library(BiocParallel)
## conffile <- system.file("scripts/config.R", package="MethylAid")
## BPPARAM <- BatchJobsParam(workers = 10,
## progressbar = FALSE,
## conffile = conffile)
## summarize(targets, batchSize = 50, BPPARAM = BPPARAM)

## ----thresholds, eval=FALSE----------------------------------------------
## visualize(exampleData,
##           thresholds = list(MU = 10.5, OP = 11.75,
##               BS = 12.75, HC = 13.25, DP = 0.95))

## ----reference, eval=FALSE-----------------------------------------------
## library(MethylAid)
## data(exampleData) ##500 samples
## library(MethylAidData)
## data(exampleDataLarge) ##2800 samples
## outliers <- visualize(exampleData, background=exampleDataLarge)
## head(outliers)

## ----combine-------------------------------------------------------------
library(MethylAid)
data(exampleData)
exampleData
combine(exampleData, exampleData)

## ----sessionInfo, results='asis', echo=FALSE-----------------------------
toLatex(sessionInfo())