The goal of the
r Biocpkg("rpx") package is to provide programmatic
access to proteomics data from R, in particular to the ProteomeXchange
(PX) central repository (see http://www.proteomexchange.org/ and
Vizcaino J.A. et al. ProteomeXchange: globally co-ordinated proteomics data submission and dissemination, Nature Biotechnology 2014, 32, 223 -- 226, doi:10.1038/nbt.2839.
Additional repositories are likely to be added in the future.
The central object that handles data access is the
class. Such an instance can be generated by passing a valid PX
experiment identifier to the
library("rpx") id <- "PXD000001" px <- PXDataset(id) px
Several attributes can be extracted from an
PXDataset instance, as
The experiment identifier, that was originally used to create the
PXDataset instance can be extracted with the
The file transfer url where the data files can be accessed can be
queried with the
The species the data has been generated the data can be obtain calling
Relevant bibliographic references can be queried with the
All files available for the PX experiment can be obtained with the
The complete or partial data set can be downloaded with the
function. The function takes an instance of class
PXDataset as first
The next argument,
list, specifies what files to download. If
missing, a menu is printed and the user can select a file. If set to
"all", all files of the experiment are downloaded. Alternatively,
numerics or logicals can also be used to subset the relevant files to
be downloaded based on the
f <- pxget(px, "PXD000001_mztab.txt") f
rpx package makes use of the
package to avoid repeatedly dowloading files. When downloaded, file
are cached, i.e. stored centrally in the package's cache
directory. Next time the
pxget() function attempts to get that file,
it will be directly retrieved from the cache instead being downloaded
Finally, a list of recent PX additions and updates can be obtained
Below, we download the fasta file from the PXD000001 dataset and load it with the Biostrings package.
fas <- grep("fasta", pxfiles(px), value = TRUE) fas f <- pxget(px, fas) f ## files available in the rpx cache
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