## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::乳胶（）## ---- inclage = false ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------库（Knitr）opts_chunk $ set（concordance = true）## --------------------------------------------------------------------------------------------------------------------------库（甲基）库（MinFidata）基于<-system.file（“ extdata”，package =“ minfidata”）目标<- read.metharray.sheet（基于）## ----------------------------------------------- # data <- summarize(targets) # visualize(data) ## ----minfiDataEPIC, cache=TRUE, message=FALSE, eval=FALSE----------------- ＃library（甲基说）＃library（minfidataepic）＃基于<-system.file（“ extdata”，package =“ minfidataepic”）＃targets <- read.metharray.sheet.sheet.sheet（基础）＃data data <-sumparize（targets）（targets）＃可视化（数据）## ---- - - - 消息= false，eval = false = false -------------------------------------------------------------------------------------------------------------＃library（甲基化）＃数据（exippledata）＃可视化（exampledata）## --------------------------------------------ET，eval = false ------------------------------------------------------------------------------------------ ＃sdrffile < - list.files（pattern =“ sdrf”，full.name = true）＃targets < - read.table（sdrffile，header，header = true，sep =“ \ t”）＃路径<-“ path_to_idat_files”＃targets < - targets [file.exists（file.path（路径，targets $ array.data.file）），]＃targets < - targets [grepl（“ red”，targets $ array.data.file），]＃，]＃targets $ basename <-gsub（“ _红色。 ## ----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())