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‎.Rbuildignore

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vignettes/vigsrc/F063721.dat-mztab.txt
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vignettes/vigsrc/P00924.fasta
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vignettes/vigsrc/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
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vignettes/vigsrc/PXD000001_mztab.txt
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vignettes/vigsrc/RforProteomics-stub.Rnw
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.gitignore
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README.md

‎.gitignore

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IMPORTANT
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sandbox/
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vignettes/Bioc2013_poster.pdf
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vignettes/Bioc2014Workshop/
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vignettes/RforProteomics.pdf
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vignettes/RProtVis.html
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vignettes/vigsrc/F063721.dat-mztab.txt
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vignettes/vigsrc/P00924.fasta
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vignettes/vigsrc/PXD000001_mztab.txt
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vignettes/vigsrc/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML
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vignettes/vigsrc/cache/
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vignettes/vigsrc/figure/
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vignettes/cache
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vignettes/figure
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vignettes/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML

‎DESCRIPTION

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Package: RforProteomics
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Type: Package
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Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication
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Version: 1.3.1
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Title: Companion package to the 'Using R and Bioconductor for
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proteomics data analysis' publication
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Version: 1.3.2
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Authors@R: c(person("Laurent", "Gatto", role=c("aut", "cre"),
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email="[email protected]"),
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person("Sebastian", "Gibb", role="ctb",
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email="[email protected]"))
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Maintainer: Laurent Gatto <[email protected]>
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Imports: R.utils, Biobase, rpx, biocViews, interactiveDisplay,
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BiocInstaller
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Suggests: mzR, MSnbase, xcms, msdata, isobar, MALDIquant,
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MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter,
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synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar,
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GO.db, org.Hs.eg.db, biomaRt, RColorBrewer, ggplot2,
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reshape2, knitr, xtable
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Depends: MSnbase
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Imports: R.utils, Biobase, rpx, biocViews, BiocInstaller,
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interactiveDisplay, shiny
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Suggests: mzR, xcms, msdata, isobar, MALDIquant (>= 1.11),
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MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter,
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synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar,
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GO.db, org.Hs.eg.db, biomaRt, RColorBrewer, ggplot2, reshape2,
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knitr, xtable
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Enhances: cleaver
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Description: This package contains code to illustrate the
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'Using R and Bioconductor for proteomics data analysis'
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manuscript. The vignette describes the code and data
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needed to reproduce the examples and figures descibed
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in the paper as well as functions to download the
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PXD000001 data files.
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Description: This package contains code to illustrate the 'Using R and
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Bioconductor for proteomics data analysis' paper. Two
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vignettes describe the code and data needed to reproduce
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the examples and figures descibed in the paper and
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functionality for proteomics visualisation.
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URL: http://lgatto.github.com/RforProteomics/
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biocViews: ExperimentData, MassSpectrometry, Proteomics, MassSpectrometryData
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biocViews: ExperimentData, MassSpectrometry, Proteomics,
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MassSpectrometryData
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License: Artistic-2.0
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VignetteBuilder: knitr
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Packaged: 2014-08-12 08:21:42 UTC; lg390
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Author: Laurent Gatto [aut, cre],
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Sebastian Gibb [ctb]

‎NAMESPACE

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importFrom("Biobase", "addVigs2WinMenu")
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importFrom("interactiveDisplay", "display")
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importFrom("BiocInstaller", "biocVersion")
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import("R.utils")
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import("biocViews")
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import("rpx")
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import("shiny")
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import("MSnbase")
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importFrom("Biobase", "addVigs2WinMenu")
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importFrom("BiocInstaller", "biocVersion")
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importFrom("R.utils", "gunzip")
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importFrom("interactiveDisplay", "display")
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export(getPXD000001mzXML,
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getPXD000001mzTab,
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getPXD000001mzData,
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getThermoHelaPRTC,
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downloadData,
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RforProteomics,
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ProtViz,
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proteomicsPackages,
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massSpectrometryPackages,
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massSpectrometryDataPackages,
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display)
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display,
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shinyMA)
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‎NEWS

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CHANGES IN VERSION 1.3.2
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------------------------
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o RforProteomics wiki on github [2014-08-02 Sat]
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o Proteomics viz vignette [2014-08-06 Wed]
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o shinyMA function [2014-08-07 Thu]
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o fix PXD000001 PRIDE urls [2014-08-08 Fri]
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o add protViz CRAN package to vig [2014-08-09 Sat]
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o RProtVis vignette needs MALDIquant >= 1.11 now [2014-08-11 Mon]
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CHANGES IN VERSION 1.3.1
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-------------------------
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------------------------
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o get biocView packages as a function [2014-07-23 Wed]
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o various typos and updates in vignette [2014-07-23 Wed]
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o functions to get packages for a biocView [2014-07-23 Wed]

‎R/PXD000001.R

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msg = paste0("Please use the rpx package to download data ",
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"from the ProteomeXchaneg repository."))
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## src <- "http://proteome.sysbiol.cam.ac.uk/lgatto/RforProteomics/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML.gz"
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src2 <- "ftp://ftp.pride.ebi.ac.uk/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"
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src2 <- "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"
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downloadData(src2, destdir, FALSE)
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}
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package = "rpx",
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msg = paste0("Please use the rpx package to download data ",
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"from the ProteomeXchaneg repository."))
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src <- "ftp://ftp.pride.ebi.ac.uk/2012/03/PXD000001/F063721.dat-mztab.txt"
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src <- "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/F063721.dat-mztab.txt"
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downloadData(src, destdir, FALSE)
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}
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package = "rpx",
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msg = paste0("Please use the rpx package to download data ",
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"from the ProteomeXchaneg repository."))
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src <- "ftp://ftp.pride.ebi.ac.uk/2012/03/PXD000001/PRIDE_Exp_Complete_Ac_22134.xml.gz"
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src <- "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PRIDE_Exp_Complete_Ac_22134.xml.gz"
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downloadData(src, destdir, TRUE)
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}
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‎R/r4prot.R

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##' Opens the package vignettes.
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##'
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##' @title Opens RforProteomics vignettes
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##' @return An instance of class \code{vignette},
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##' as returned by \code{\link{vignette}}
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##' @title Opens the RforProteomics vignette
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##' @return An instance of class \code{vignette}. Used for its side
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##' effect, opening the vignette.
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##' @author Laurent Gatto
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RforProteomics <- function()
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vignette("RforProteomics", package = "RforProteomics")
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##' Opens the visualisation vignette
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##'
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##' @title Opens the visualisation vignette
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##' @return An instance of class \code{vignette}. Used for its side
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##' effect, opening the vignette.
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##' @author Laurent Gatto
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ProtViz <- function()
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vignette("ProtViz", package = "RforProteomics")
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##' Finds the package names that have a specific biocView.
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##'

‎R/shinyMA.R

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shinyMA <- function() {
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qnt <- NULL
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data(qnt, envir = environment())
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findClosest <- function(input) {
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if (is.null(input$plotma_click)) {
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1
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} else {
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pt <- c(input$plotma_click$x, y=input$plotma_click$y)
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sqdists <- colMeans((t(fData(qnt)[, c("baseMean", "log2FC")]) - pt)^2)
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which.min(sqdists)
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}
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}
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app <- list(
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ui = fluidPage(
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titlePanel("MA-plot + expression plot with shiny"),
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## flow layout fills out left to right then down
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flowLayout(
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plotOutput("plotma", clickId="plotma_click", width=400, height=400),
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plotOutput("plotcounts", width=400, height=400)
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)
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),
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server = function(input, output) {
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## MA-plot
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output$plotma <- renderPlot({
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## process possible input
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idx <- findClosest( input )
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par(mar = c(5,5,3,2), cex.lab = 1.5)
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## MA-plot of all genes
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plot(fData(qnt)$baseMean, fData(qnt)$log2FC,
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xlab = "A", ylab = "M")
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grid()
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abline(v = 0)
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## add circle for the selected point
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points(fData(qnt)$baseMean[idx],
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fData(qnt)$log2FC[idx],
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col="dodgerblue", cex=3, lwd=3)
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})
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## counts plot
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output$plotcounts <- renderPlot({
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## process possible input
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idx <- findClosest( input )
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par(mar = c(5,5,3,2), cex.lab = 1.5)
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## plot the counts for the selected gene
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i <- exprs(qnt)[idx, ]
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plot(1:6, i,
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col = c("red", "steelblue")[as.numeric(qnt$conditions)],
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pch = 19,
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main = paste0(fData(qnt)$accession[idx],
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" (", fData(qnt)$sequence[idx], ")"),
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xlab = "samples",
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ylab = "intensity")
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abline(h = mean(i[qnt$conditions == "A"]),
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col = "red", lty = "dotted")
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abline(h = mean(i[qnt$conditions == "B"]),
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col = "steelblue", lty = "dotted")
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})
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}
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)
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runApp(app)
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}

‎R/zzz.R

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.onAttach <- function(libname, pkgname) {
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packageStartupMessage(paste0("This is the 'RforProteomics' version ",
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utils::packageVersion("RforProteomics"), ".\n",
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"Run 'RforProteomics()' in R or visit \n",
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"'http://lgatto.github.com/RforProteomics/' to get started.\n\n",
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sep=""))
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addVigs2WinMenu("synapter")
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packageStartupMessage(paste0("\nThis is the 'RforProteomics' version ",
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utils::packageVersion("RforProteomics"), ".\n\n",
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" To get started, visit\n",
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" http://lgatto.github.com/RforProteomics/\n\n",
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" or, in R, open package vignettes by typing\n",
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" RforProteomics() # R/Bioc for proteomics overview\n",
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" ProtViz() # R/Bioc for proteomics visualisation\n\n"))
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addVigs2WinMenu("RforProteomics")
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}
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‎README.md

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proteomics, in particular by facilitating interoperability between
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their software. The
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[rbioc-sig-proteomics](https://groups.google.com/forum/#!forum/rbioc-sig-proteomics)
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group has tentatively been set up to provide an question and
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discussion forum for interested parties. Do not hesitate to
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group has tentatively been set up to provide a forum for questions and
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discussion for interested parties. Do not hesitate to
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[get in touch](http://proteome.sysbiol.cam.ac.uk/lgatto/) for
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questions, comments or further suggestions.
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questions, comments or further suggestions. Note taking about
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plans/ideas/direction for R/Bioc and proteomics can be contributed to
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the
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[`RforProteomics` wiki](https://github.com/lgatto/RforProteomics/wiki).
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## Data and vignette
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The package also distributes a set of function to access data from the
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[ProteomeXchange](http://www.proteomexchange.org/)
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The package uses the dataset
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[`PXD000001`](http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000001)
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data, used in several examples, as well as a detailed document
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from the [ProteomeXchange](http://www.proteomexchange.org/) repository
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in several examples. The data can be queries and downloaded from `R`
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with the
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[`rpx`](http://bioconductor.org/packages/release/bioc/html/rpx.html)
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package. The `RforProteomics` vignette is a detailed document
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containing the exact code to reproduce all the analyses presented in
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the manuscript as well as other application examples. The latter
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document is called the package vignette, and can be accessed once the
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package is installed (see below) with the `RforProteomics()`
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function. Alternatively, the vignette can be downloaded as a pdf file
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the manuscript as well as other application examples. It can be
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accessed once the package is installed (see below) with the
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`RforProteomics()` function. Alternatively, the vignette can be
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downloaded as a pdf file
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[here](http://bioconductor.org/packages/devel/data/experiment/vignettes/RforProteomics/inst/doc/RforProteomics.pdf).
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A second vignette, `RProtVis` is currently underdevelopmenet and will
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focus on the visualisation of mass spectrometry and proteomics data
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with `R` and Bioconductor. It can be accessed with the `RProtViz()`
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function.
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## Installation
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The package is now available in
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The package is available on
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[Bioconductor](http://bioconductor.org/packages/devel/data/experiment/html/RforProteomics.html)
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version 2.13. To install the package and its documentation, start `R`
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(>= `3.0.0` required) and type:
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(version >= 2.13). To install the package and its documentation, start
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`R` (>= `3.0.0` required) and type:
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```c
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source("http://bioconductor.org/biocLite.R")
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biocLite("RforProteomics")
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```
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To install all dependencies (78 packages, including `RforProteomics`)
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To install all dependencies (75+ packages, including `RforProteomics`)
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and reproduce the code in the vignette, replace the last line in the
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code chunk above with:
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‎data/qnt.rda

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Binary file not shown.

‎man/ProtViz.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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\name{ProtViz}
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\alias{ProtViz}
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\title{Opens the visualisation vignette}
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\usage{
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ProtViz()
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}
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\value{
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An instance of class \code{vignette}. Used for its side
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effect, opening the vignette.
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}
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\description{
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Opens the visualisation vignette
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}
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\author{
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Laurent Gatto
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}
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‎man/RforProteomics.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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\name{RforProteomics}
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\alias{RforProteomics}
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\title{Opens RforProteomics vignettes}
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\title{Opens the RforProteomics vignette}
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\usage{
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RforProteomics()
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}
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\value{
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An instance of class \code{vignette},
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as returned by \code{\link{vignette}}
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An instance of class \code{vignette}. Used for its side
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effect, opening the vignette.
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}
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\description{
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Opens the package vignettes.

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