## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, eval = FALSE) libv <- c("minfiData", "HDF5Array", "minfi") sapply(libv, library, character.only = TRUE) ## ----------------------------------------------------------------------------- # rg.hm450k <- get(data("RGsetEx")) ## ----------------------------------------------------------------------------- # rg.epic <- convertArray(rg.hm450k, "IlluminaHumanMethylationEPIC") ## ----------------------------------------------------------------------------- # ms.hm450k <- preprocessRaw(rg) # make MethylSet # ms.hm450k <- mapToGenome(ms.hm450k) # make GenomicMethylSet ## ----------------------------------------------------------------------------- # gr.hm450k <- GenomicMethylSet(gr = granges(ms.hm450k), # Meth = getMeth(ms.hm450k), # Unmeth = getUnmeth(ms.hm450k), # annotation = annotation(ms.hm450k)) ## ----------------------------------------------------------------------------- # saveHDF5SummarizedExperiment(gr.hm450k, dir = "gr_h5se_new") ## ----------------------------------------------------------------------------- # gr.h5se <- loadHDF5SummarizedExperiment(dir = "gr_h5se_new") ## ----eval = FALSE------------------------------------------------------------- # # get flat files # m.beta <- getBeta(gr.h5se) # anno <- as.data.frame(getAnnotation(gr.h5se)) # coldata <- as.data.frame(colData(gr.h5se)) # # save flat files # save(m.beta, file = "mbeta_new.rda") # save(anno, file = "anno_new.rda") # save(coldata, file = "coldata_new.rda") ## ----eval = FALSE------------------------------------------------------------- # write.table(m.beta, file = "mbeta_new.txt") # write.csv(m.beta, file = "mbeta_new.csv") # data.table::fwrite(m.beta, file = "mbeta_new.txt") ## ----eval = FALSE------------------------------------------------------------- # save(rg, file = "rg_new.rda") # save(gm, file = "gm_new.rda") # save(gr, file = "gr_new.rda") ## ----------------------------------------------------------------------------- # rg.h5se <- rg.h5se[seq(1000),] # subset the h5se object # quickResaveHDF5SummarizedExperiment(rg.h5se) # rapidly update stored file