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# Cross Matching Example

```{r setup, include=FALSE}
library(knitr)
opts_chunk$set(fig.height=10, fig.width=14, fig.path="figure/crossmatching/", cache=TRUE, autodep=TRUE, tidy=FALSE)
```
## Default Synapter Preprocessing

(same as in `synergise`)

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importSIMS <- function(path) {
  stopifnot(file.exists(path) && file.info(path)$isdir)

  ## find all txt files 
  files <- list.files(path, pattern="^.*\\.txt$", full.names=TRUE, recursive=TRUE)
  files <- normalizePath(files)

  ## read metadata (first 8 lines) of the SIMS file
  ll <- lapply(files, function(f)readLines(f, n=8))

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

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

fasfile <- synapterdata::getFasta()
mstrfile <- synapterdata::getMaster()
pepfile <- synapterdata::getMSeFinalPeptide()[2]

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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

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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")

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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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\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}

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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")))

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library("MALDIquant")

data("fiedler2009subset")

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

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library("shiny")

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

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

data("fiedler2009subset")

convertYlim <- function(lim, fun) {