## ----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") ## ----Chromatograms--------------------------------------------------------- getClass("Chromatograms") ## ----msl------------------------------------------------------------------- getClass("MSnSetList") ## ----si-------------------------------------------------------------------- sessionInfo()