/rawDiag

Bring Mass Spectrometry Data to Life; Multi-platform, Fast and Colorful R package.

Primary LanguageRGNU General Public License v3.0GPL-3.0

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 System Requirements

a Windows/Linux/MacOSX x64 platform

1.1 .NET Framework and R

1.2 The New RawFileReader .Net assembly from Thermo Fisher Scientific

If your installation does not work with the below-mentioned instructions, do not hesitate to request a ready to run R package from the authors via Email, SUBJECT request rawDiag package.

Due to licensing reasons, we currently not allowed to distribute Thermo Fisher Scientific software with the rawDiag package (we hope that this will change soon). 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.

1.3 Platforms and versions the software has been tested on

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

platform platform version R version note
Linux Debian 8 (jessie) 3.4.3 Demo system
Linux Debian 10 (buster) 3.5.0 CP
Linux bioconductor/devel_proteomics2 2017-12-31 r73996 dockerhub no RawFileReader support
Windows 7 x64 3.4.1 CT
Windows 10 x64 3.4.4 CP virtual box
Windows Server 2012 R2 x64 3.4.4 CP
Windows 10 x64 3.4.3 WEW
Windows 10 x64 R Open 3.5.0 WEW
MacOSX 10.13.5 (17F77) 3.4.2 CP
MacOSX 10.11.6 (15G20015) 3.4.3 JG
MacOSX 10.13.4 (17E202) 3.4.4 CP

2 Installation guide

2.1 Instructions

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

all OS

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)

2.2 Typical install time on a "normal" desktop computer

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

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