cpanse/rawdiag repository overview

⁠rawDiag

an R package supporting rational LC-MS method optimization for bottom-up proteomics on multiple OS platforms

main features:

1. multiplatform and fast reading through using The New RawFileReader from Thermo Fisher Scientific⁠.
2. uses latest visualization generation through using Rs ggplot2⁠ package.
3. provides an R interface to your instrument raw data.
4. ships with an example shiny application⁠.

⁠1 Requirements

⁠1.1 Thermo License agreement

accept the Thermo Fisher RawFileReader License agreement⁠.

⁠1.2 System Requirements

a Windows/Linux/MacOSX x64 platform

.NET Framework and R

• https://www.mono-project.com/⁠ (>4.0.22) for (Linux and MacOSX),
• .NET Framework 4.5.1 or higher (Windows),
• R (>3.4.0); please do not use R (3.5.0) on Windows! There is an system2 issue,
• install https://CRAN.R-project.org/package=devtools⁠
• if you want support for Open File Standards⁠ install the mzR⁠ package.

⁠2 Installation guide

To ensure the proper function of this R package please check if all the requirements⁠ are fullfilled prior to using it.

⁠2.1 Install

run R

#R
  
# R package requirements
pkgs <- c( 'devtools',
  'dplyr',
  'ggplot2',
  'hexbin',
  'magrittr',
  'parallel',
  'protViz',
  'rmarkdown',
  'RSQLite',
  'scales',
  'shiny',
  'tidyr',
  'tidyverse')
pkgs <- pkgs[(!pkgs %in% unique(installed.packages()[,'Package']))]
if(length(pkgs) > 0){install.packages(pkgs)}

# Installation of rawDiag
install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawDiag_0.0.10.tar.gz')

# Testing - "Hello, world!"
library(rawDiag)
(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))
system.time(RAW <- read.raw(file = rawfile))
dim(RAW)
summary.rawDiag(RAW)
PlotScanFrequency(RAW)

# read all dimensions
dim(RAW)
RAW <- read.raw(file = rawfile, rawDiag = FALSE)
dim(RAW)

⁠2.2. If you have problems

If your installation does not work with the below-mentioned instructions, do not hesitate to contact us via Email, SUBJECT help request rawDiag package⁠.

Please include the output of the sessInfo() command line call.

sessionInfo()

⁠2.3 Install from GitHub (only for developers)

the following code downloads and installs the R package from the Github without the required third party .dll files: please note: due to the data size (>=40MB) download can take a while

# install.packages("devtools")
library("devtools")
devtools::install_github("fgcz/rawDiag", build_vignettes = FALSE)

The New RawFileReader from Thermo Fisher Scientific⁠ has to be downloaded and installed separately in order to be able to directly read Thermo raw-files (by using the R function read.raw).

To install the New RawFileReader .Net assembly⁠ follow the installation instructions provided by Thermo Fisher Scientific.

⁠2.4 Typical install time on a "normal" desktop computer

• Thermo RawFileReader dll: 1sec to 30 minutes
• the rawDiag package through github: 10 minutes

⁠2.5 Platforms and versions the software has been tested on

The package JPR.R1⁠ release has been tested on the following platforms using RStudio⁠:

⁠3 Demonstration

⁠3.1 R commandline code snippet

"Hello; World!" example on the R command line

library(rawDiag)
data(WU163763)
PlotScanFrequency(WU163763, method='overlay')
PlotPrecursorHeatmap(WU163763)
PlotMassDistribution(WU163763

⁠3.2 An interactive shiny example

⁠in your local R shell

# install.packages("shiny")
# install.packages("DT")
library(shiny)
rawDiag_shiny <- system.file('shiny', 'demo', package = 'rawDiag')
shiny::runApp(rawDiag_shiny, display.mode = 'normal')

⁠using the docker image

source: dockerhub⁠

docker pull cpanse/rawdiag \
&& docker run -it -p 8787:8787 cpanse/rawdiag R -e "library(shiny); \
   rawDiag_shiny <- system.file('shiny', 'demo', package = 'rawDiag'); \
   shiny::runApp(rawDiag_shiny, display.mode = 'normal', port=8787, host='0.0.0.0')"

connect with your web browser to http://yourdockerhostname:8787

⁠3.3 using the read.raw method

taken from the ?read.raw man page.

(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))
system.time(RAW <- read.raw(file = rawfile))
 
summary.rawDiag(RAW)
PlotScanFrequency(RAW)
     
dim(RAW)
# now  read all dimensions
RAW <- read.raw(file = rawfile, rawDiag = FALSE)
dim(RAW)

⁠4 Instructions for use

read the vignettes.

browseVignettes('rawDiag')

the documentation of the function is available through the R man pages.

⁠5 Useful links

• http://planetorbitrap.com/rawfilereader⁠

• screen recording (3:02 minutes, size 47MB, no audio track)⁠

• shiny demo on our compute server⁠

• rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics Christian Trachsel, Christian Panse, Tobias Kockmann, Witold Eryk Wolski, Jonas Grossmann, Ralph Schlapbach bioRxiv 304485; doi: https://doi.org/10.1101/304485⁠ (manuscript submitted to Journal of Proteome Research; pr-2018-001736).

• MassIVE MSV000082389⁠

• ASMS 2018 poster as PDF(1.8M, md5=dab9388c1a465d931e9d2345119a2827)⁠