## ----citation,eval=FALSE------------------------------------------------------ # toBibtex(citation("minfi")) ## ----dependencies, warning=FALSE, message=FALSE------------------------------- library(minfi) library(minfiData) ## ----RGsetEx------------------------------------------------------------------ RGsetEx ## RGsetEx: RGChannelSet, 622,399 features MsetEx <- preprocessRaw(RGsetEx) ## MsetEx: MethylSet, 485,512 features GMsetEx <- mapToGenome(MsetEx) ## GMsetEx: GenomicMethylSet, 485,512 features ## ----baseDir------------------------------------------------------------------ baseDir <- system.file("extdata", package = "minfiData") list.files(baseDir) ## ----baseDir2----------------------------------------------------------------- list.files(file.path(baseDir, "5723646052")) ## ----sheet-------------------------------------------------------------------- targets <- read.metharray.sheet(baseDir) targets ## ----BasenameColumn>---------------------------------------------------------- sub(baseDir, "", targets$Basename) ## ----readingTargets----------------------------------------------------------- RGset <- read.metharray.exp(targets = targets) ## ----pData-------------------------------------------------------------------- RGset pd <- pData(RGset) pd[,1:4] ## ----read2-------------------------------------------------------------------- RGset2 <- read.metharray.exp(file.path(baseDir, "5723646052")) RGset3 <- read.metharray.exp(baseDir, recursive = TRUE) ## ----sampleSheet2------------------------------------------------------------- targets2 <- read.csv(file.path(baseDir, "SampleSheet.csv"), stringsAsFactors = FALSE, skip = 7) targets2 ## ----Basename----------------------------------------------------------------- targets2$Basename <- file.path(baseDir, targets2$Sentrix_ID, paste0(targets2$Sentrix_ID, targets2$Sentrix_Position)) ## ----annotation--------------------------------------------------------------- annotation(RGsetEx) ## ----sessionInfo, results='asis', echo=FALSE---------------------------------- toLatex(sessionInfo())