## ----env, echo=FALSE, message=FALSE---------------------------------------- suppressPackageStartupMessages(library("BiocStyle")) suppressPackageStartupMessages(library("MSnbase")) suppressPackageStartupMessages(library("BiocParallel")) ## ----msdata---------------------------------------------------------------- library("msdata") f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz") basename(f) ## ----verb------------------------------------------------------------------ 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")