## ----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())