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.

First, we need to install devtools:

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

Then we just call

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

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.

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))

Some things to be done, sooner than later:

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

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