inst/doc/v05-MSnbase-development.R

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

## ----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()