## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------ BiocStyle::latex() ## ----'setup', include = FALSE, cache = FALSE----------------------------- library("knitr") opts_chunk$set(fig.align = 'center', fig.show = 'hold', par = TRUE, prompt = FALSE, comment = NA) options(replace.assign = TRUE, width = 65) ## ----environment, cache=FALSE, echo=FALSE-------------------------------- suppressPackageStartupMessages(library(MSnbase)) ## ----pSet---------------------------------------------------------------- getClass("pSet") ## ----MSnExp-------------------------------------------------------------- getClass("MSnExp") ## ----MSnSet-------------------------------------------------------------- getClass("MSnSet") ## ----MSnProcess---------------------------------------------------------- getClass("MSnProcess") ## ----MIAPE--------------------------------------------------------------- getClass("MIAPE") ## ----Spectrum------------------------------------------------------------ getClass("Spectrum") ## ----Spectrum1----------------------------------------------------------- getClass("Spectrum1") ## ----Spectrum2----------------------------------------------------------- getClass("Spectrum2") ## ----ReporterIons-------------------------------------------------------- getClass("ReporterIons") ## ----NAnnotatedDF-------------------------------------------------------- getClass("NAnnotatedDataFrame") ## ----sessioninfo, results='asis', echo=FALSE, cache=FALSE---------------- toLatex(sessionInfo())