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.
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.
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)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.
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.