prideR

An R package to obtain data from the EMBL-EBI Proteomics Repository Identifications Database (PRIDE Archive and PRIDE Cluster). It uses its RESTful Web Services at PRIDE Archive WS and PRIDE Cluster WS for that purpose.

Currently, the following domain entities are supported:

• Projects as S4 objects, including methods to get them from PRIDE by accession and as.data.frame
• Assays as S4 objects, including methods to get them from PRIDE by accession and as.data.frame
• Files as S4 objects, including methods to get them from PRIDE by project and assay accession and as.data.frame
• Protein identifications associated with a project, as S4 objects, including methods to get them from PRIDE by project accession and as.data.frame
• PSM identifications associated with a project, as S4 objects, including methods to get them from PRIDE by project accession and as.data.frame
• PRIDE Cluster ClusterSummary, as S4 objects and as as.data.frame.

Installation

First, we need to install devtools:

install.packages("devtools")
library(devtools)

Then we just call

install_github("PRIDE-R/prideR")
library(prideR)

Examples

PRIDE Archive

Get project PXD000001 summary:

get.ProjectSummary("PXD000001")

Search for at most 20 projects by term blood. The results are returned as a list of ProjectSummary objects:

search.list.ProjectSummary("blood",0,20)

Get the list of results from it:

project.list(search.list.ProjectSummary("blood",0,20))

Get them as a data.frame:

as.data.frame(search.list.ProjectSummary("blood",0,20))

Get the first 50 Proteins for project PXD000001 as a list of ProteinDetail objects:

protein.list(list.ProteinDetailList("PXD000001", 0, 50))

Or as a data.frame:

as.data.frame(list.ProteinDetailList("PXD000001",0, 50))

Plot some counts:

plot(list.ProteinDetailList("PXD000001",0, 50))

Get 5 PSMs for project PXD000001 as a list of PsmDetail objects:

get.list.PsmDetail("PXD000001", 5)

There are also count methods for each of the PRIDE Archive entitites.

PRIDE Cluster

Get page 0 with a size of 20 clusters for peptide sequence LSVDYGK:

search.ClusterSearchResults("LSVDYGK", 0, 20)

As a data frame:

as.data.frame(search.ClusterSearchResults("LSVDYGK", 0, 20))

Plot results:

plot(search.ClusterSearchResults("LSVDYGK", 0, 20))

Future Works

Some things to be done, sooner than later:

• Check mandatory parameters
• Deal with SpectrumDetail entities when available

About us

Find out about us in our GitHub profiles:
Jose A. Dianes
Rui Wang

How to cite

• Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., ... & Hermjakob, H. (2013). The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic acids research, 41(D1), D1063-D1069. HERE