## ----include=FALSE------------------------------ library(knitr) opts_chunk$set(tidy=FALSE，cache = true，size ='scriptSize'）## ----设置，eval = true，hide = true，echo = false -------选项（'width'= 50）## -------------------------------------------loadlibraries，eval = true ------------------抑制PackagestArtupMessages（require（'yendylumi'））suppresspackagestArtupMessages（require（'tcgamethylation450k'）suppresspackageStartupMessages（require（'firect）（'fdb。InfiniumMethylation.hg19')) ## ----loadData, eval=TRUE------------------------ ## read in 10 BRCA IDATs idatPath <-system.file（'extdata/idat'，package ='tcgamethylation450k'）mset450k <-menylumidat（getbarcodes（path = iDatpath），idatpath = idatpath = idatpath）samplenames（mset450k）（mset450k）））show（mset450k）## ----控制，图。width = 5，图。数据集，by.type参数设置为false ##位置效应将显示为像波的模式p <-qc.probe.plot（mset450k，by.type = true = true = true）print（p）## ----预处理，eval = true ------------------------------------------------------------------------------------ proc <-Stripoob（strumanizemethylumiset（甲基菌）（MSET450K）））## ---- controls2，图。width = 5，图。Height= 7，quient = true，echo，echo = true，cache = false---库（ggplot2）p2 <-qc.probe。suppresspackagestArtupMessages（require（lumi））mset450k.lumi < - as（mset450k.proc，'ridymim'）show（mset450k.lumi）## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------和back < - as（mset450k.lumi，'yenylumiset'）show（mset450k andback）## ---- coerceminfi，eval = true = true ---------------------------------------------------------------------------------------------抑制PackagestArtupMessages（require（fdb.infiniummethylation.hg19））rgset450k < - as（mset450k，'rgchannelset'）show（rgset450k）true -------------------------抑制PackagestArtupMessages（require（minfi））抑制PackagestArtupMessages（require（Illuminahumanmethylation450Kanno.ilmn12.hg19））grset450k <-- met450k.andback）Exchroms <-granges（seqnames = c（'Chrx'，'Chry'），iranges（start = c（1，1），end = c（155270560，59373566）），strand = c（'*'，'，'*''）摘要（subsetByoverLaps（grset450k，sexchroms））DIM（subsetBoyoverLaps（grset450k，sexchroms））## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ## perhaps more topical: suppressPackageStartupMessages(require(TxDb.Hsapiens.UCSC.hg19.knownGene)) suppressPackageStartupMessages(require(Homo.sapiens)) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene KDM6AEntrezID=org.Hs.egSYMBOL2EG[['KDM6A']] txs.KDM6A <- transcriptsBy(txdb, 'gene')[[KDM6AEntrezID]] tss.KDM6A <- unique(resize(txs.KDM6A, 1, fix='start')) ## two start sites promoters.KDM6A <- flank(tss.KDM6A, 100) ## an arbitrary distance upstream show( subsetByOverlaps(grSet450k, promoters.KDM6A) ) ## probes in this window ## ----results='asis'----------------------------- toLatex(sessionInfo())