## ------ env，echo = false，消息= false ----------------------------------------------------------------------------------------------------------------------------------抑制PackagestArtupMessages（库（“ BiocStyle”））suppresspackagestArtupMessages（库（“ msnbase”））suppresspackagestartupmessages（library（“ biocparallel”）--------------------------------------------------------------------------------------------------库（“ MSDATA”）f <-msdata :: proteomics（full.names = true，pattern =“ tmt_erwinia_1ulsike_top10hcd_isol2_isol2_45stepped_60min_01.01.mzml.gz”----------------------------------------------------------------------------------------------------------- library("MSnbase") setMSnbaseVerbose(FALSE) ## ----read1-------------------------------------------------------------------- system.time(inmem <- readMSData(f, msLevel = 2, mode = "inMemory", centroided = TRUE)) ## ----read2-------------------------------------------------------------------- system.time(ondisk <- readMSData(f, msLevel = 2, mode = "onDisk", centroided = TRUE)) ## ----equal12------------------------------------------------------------------ all.equal(inmem, ondisk) ## ----------------------------------------------------------------------------- library("pryr") object_size(inmem) object_size(ondisk) ## ----plot0, eval=FALSE-------------------------------------------------------- # plot(inmem[[200]], full = TRUE) # plot(ondisk[[200]], full = TRUE) ## ----plot1, echo=FALSE, fig.wide=TRUE, fig.cap = "Plotting in-memory and on-disk spectra"---- suppressMessages(requireNamespace("gridExtra")) gridExtra::grid.arrange(plot(inmem[[200]], full = TRUE), plot(ondisk[[200]], full = TRUE), ncol = 2) ## ----mb, cache=TRUE----------------------------------------------------------- library("microbenchmark") mb <- microbenchmark(spectra(inmem), inmem[[200]], spectra(ondisk), ondisk[[200]], times = 10) mb ## ----subset------------------------------------------------------------------- i <- sample(length(inmem), 100) system.time(inmem[i]) system.time(ondisk[i]) ## ----qnt, cache=TRUE---------------------------------------------------------- system.time(eim <- quantify(inmem[1:100], reporters = TMT6, method = "max")) system.time(eod <- quantify(ondisk[1:100], reporters = TMT6, method = "max")) all.equal(eim, eod, check.attributes = FALSE) ## ----vigs, eval=FALSE--------------------------------------------------------- # vignette(package = "MSnbase")