Introduction
The
RforProteomics package
distributes and extends the use-cases described in the Using R and
Bioconductor for proteomics data analysis manuscript
(pubmed and
pre-print). The package illustrates
how R and a selection of dedicated packages that can be used to
access mass-spectrometry proteomics data, manipulate and visualise it,
how to process label-free and labelled quantitative data and how to
analyse the quantitation data.
The package will be updated beyond the content of the manuscript to
keep up-to-date with progress in the area. The
github page can be used to
edit the wiki and file new issues related to the package itself of
general needed for proteomics that should be addressed in R.
NB: I you are interested in R packages for mass spectrometry-based proteomics and metabolomics, see also the R for Mass Spectrometry initiative packages and the tutorial book
It would be great if this work could stimulate a wider participation
to use R and develop R packages for proteomics and promote
interaction between computational biologists working in the field of
proteomics, in particular by facilitating interoperability between
their software. The official Bioconductor support
site is the channel of choice to
ask questions about specific Bioconductor packages.
Data and vignette
The package uses the
dataset
PXD000001 from
the ProteomeXchange repository in
several examples. The data can be queried and downloaded from R with
the
rpx
package. The RforProteomics vignette is a detailed document
containing the exact code to reproduce all the analyses presented in
the manuscript as well as other application examples. It can be
accessed once the package is installed (see below) with the
RforProteomics() function. Alternatively, the vignettes can be read
online
here and
here.
A second vignette, RProtVis focuses on the visualisation of mass
spectrometry and proteomics data with R and Bioconductor. From R,
it is currently only available with Bioconductor >= 3.0 using the
RProtViz() function. It can also be consulted
on-line
on the 'RforProteomics' development version page.
Installation
The package is available on
Bioconductor
(version >= 2.13). To install the package and its documentation, start
R (>= 3.0.0 required) and type:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("RforProteomics")
To install all dependencies (75+ packages, including RforProteomics)
and fully reproduce the code in the vignettes, replace the last line
in the code chunk above with:
BiocManager::install("RforProteomics", dependencies = TRUE)
Collaborative editing
The community and package authors are invited to contribute to the package. If you have or know of a package of interest, please fork the repository, add a new section to the vignette and send a pull request. If you update the vignette, please also add yourself as a contributor to the package.
Help
To obtain help or additional information about the RforProteomics
package and about the packages presented in the vignette or
manuscript, please use the Bioconductor support
site.
For general resources about R, see the corresponding section in the
vignettes and the
TeachingMaterial
repository.