sgibb

fwhm <- function(spectrum, peaks) {

  ## work horse
  .fwhm <- function(spectrum, i) {
    n <- length(spectrum)
    left <- ifelse(i <= 1, 1, i)
    right <- ifelse(i >= n, n, i)
    
    hm <- spectrum@intensity[i]/2
    

sgibb

## code to import peaks from Bruker xml files

importBrukerXml <- function(file) {
  require("MALDIquant")

  ## read file
  r <- readLines(file)

  ## remove useless stuff
  r <- gsub(pattern="^.*<ms_peaks>|</ms_peaks>.*$", replacement="", x=r)

sgibb

library("shiny")

library("MALDIquant")

data("fiedler2009subset")

shinyServer(function(input, output) {

  output$plotBaseline <- renderPlot({
    plot(fiedler2009subset[[1]])

sgibb

library("shiny")

library("MALDIquant")
library("MALDIquantForeign")

options(shiny.maxRequestSize=200*1024^2)

data("fiedler2009subset")

convertYlim <- function(lim, fun) {

sgibb

library("MALDIquant")

data("fiedler2009subset")

## preprocessing
spectra <- transformIntensity(fiedler2009subset, sqrt)
spectra <- transformIntensity(spectra, savitzkyGolay)
spectra <- removeBaseline(spectra)
peaks <- detectPeaks(spectra)

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library("MALDIquant")

#' create toy example
p <- c(p1=createMassPeaks(mass=c(1, 1.5, 10), intensity=c(1, 2, 1),
                          metaData=list(name="p1")),
       p2=createMassPeaks(mass=c(0.9, 10.1), intensity=c(1, 1),
                          metaData=list(name="p2")),
       p3=createMassPeaks(mass=c(1.1, 9.9), intensity=c(1, 1),
                          metaData=list(name="p3")))

sgibb

\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{Bioconductor}[2013/07/01 Bioconductor vignette style]

%%     -I would wish to know how to make this work-
%% \DeclareOption{pdftitle}{\PassOptionsToPackage{pdftitle}{hyperref}}
%% \DeclareOption{pdfauthor}{\PassOptionsToPackage{pdfauthor}{hyperref}}
%% \ExecuteOptions{pdftitle,pdfauthor}
%% \ProcessOptions

\PassOptionsToPackage{usenames,dvipsnames}{color}

sgibb

convertFile <- function(inputFile, outputFile,
                        fromEncoding="UTF-8", toEncoding="ASCII") {
  stopifnot(file.exists(inputFile))
  input <- readLines(inputFile, encoding=fromEncoding)
  output <- iconv(input, from=fromEncoding, to=toEncoding)
  return(writeLines(output, outputFile))
}

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library("RNetCDF")

nc <- create.nc("tiny.cdf")

dim.def.nc(nc, "scan_number", 2)
dim.def.nc(nc, "point_number", 10, unlim=TRUE)

var.def.nc(nc, "scan_index", "NC_INT", "scan_number")
var.def.nc(nc, "point_count", "NC_INT", "scan_number")
var.def.nc(nc, "scan_acquisition_time", "NC_DOUBLE", "scan_number")

sgibb

library("synapter")
library("synapterdata")

## map some private functions to global NAMESPACE
doHDMSePredictions <- synapter:::doHDMSePredictions
error.ppm <- synapter:::error.ppm
findMSeEMRTs <- synapter:::findMSeEMRTs

########################################################################### 
## some boring stuff to prepare the Synapter object