an R package supporting rational LC-MS method optimization for bottom-up proteomics on multiple OS platforms
main features:
- multiplatform and fast reading through using The New RawFileReader from Thermo Fisher Scientific.
- uses latest visualization generation through using Rs ggplot2 package.
- provides an R interface to your instrument raw data.
- ships with an example shiny application.
a Windows/Linux/MacOSX x64 platform
- 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.
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.
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 |
To ensure the proper function of this R package please check if all the requirements are fullfilled prior to using it.
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)
- Thermo RawFileReader dll: 1sec to 30 minutes
- the rawDiag package through github: 10 minutes
"Hello; World!" example on the R command line
library(rawDiag)
data(WU163763)
PlotScanFrequency(WU163763, method='overlay')
PlotPrecursorHeatmap(WU163763)
PlotMassDistribution(WU163763
# install.packages("shiny")
# install.packages("DT")
library(shiny)
rawDiag_shiny <- system.file('shiny', 'demo', package = 'rawDiag')
shiny::runApp(rawDiag_shiny, display.mode = 'normal')
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
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)
read the vignettes.
browseVignettes('rawDiag')
the documentation of the function is available through the R man pages.
-
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).
-
ASMS 2018 poster as PDF(1.8M, md5=dab9388c1a465d931e9d2345119a2827)