## ----environment, echo=FALSE-------------------------------------------------- suppressPackageStartupMessages(library("MSnbase")) suppressPackageStartupMessages(library("BiocStyle")) ## ----include_forword, echo=FALSE, results="asis"------------------------------ cat(readLines("./Foreword.md"), sep = "\n") ## ----include_bugs, echo=FALSE, results="asis"--------------------------------- cat(readLines("./Bugs.md"), sep = "\n") ## ----pSet--------------------------------------------------------------------- getClass("pSet") ## ----MSnExp------------------------------------------------------------------- getClass("MSnExp") ## ----OnDiskMSnExp------------------------------------------------------------- getClass("OnDiskMSnExp") ## ----MSnSet------------------------------------------------------------------- getClass("MSnSet") ## ----as----------------------------------------------------------------------- data(msnset) class(msnset) class(as(msnset, "ExpressionSet")) data(sample.ExpressionSet) class(sample.ExpressionSet) class(as(sample.ExpressionSet, "MSnSet")) ## ----MSnProcess--------------------------------------------------------------- getClass("MSnProcess") ## ----MIAPE-------------------------------------------------------------------- getClass("MIAPE") ## ----Spectrum----------------------------------------------------------------- getClass("Spectrum") ## ----Spectrum1---------------------------------------------------------------- getClass("Spectrum1") ## ----Spectrum2---------------------------------------------------------------- getClass("Spectrum2") ## ----ReporterIons------------------------------------------------------------- getClass("ReporterIons") ## ----Chromatogram------------------------------------------------------------- getClass("Chromatogram") ## ----MChromatograms----------------------------------------------------------- getClass("MChromatograms") ## ----msl---------------------------------------------------------------------- getClass("MSnSetList") ## ----si----------------------------------------------------------------------- sessionInfo()