inst/doc/MethylAid.R

In MethylAid: Visual and interactive quality control of large Illumina DNA Methylation array data sets

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

## ----include=FALSE---------------------------------------------------------
library(knitr)
opts_chunk$set(
concordance=TRUE
)

## ----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)

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