Class "PXDataset"

Description

An S4 class to store and access information about ProteomeXchange (PX) data sets. Schema versions 1.0, 1.1 and 1.2 are supported and are documented on the PX code repository: https://code.google.com/p/proteomexchange/source/browse/schema/

Objects from the Class

Objects can be created with the constructor PXDataset.

Slots

id:

Object of class "character" storing the datasets unique identifier. Can be accessed with pxid().

formatVersion:

Object of class "character" storing the version of the ProteomeXchange schema.

Data:

Object of class "XMLNode" storing the ProteomeXchange description as XML node tree.

Methods

pxfiles

signature(object = "PXDataset"): return a character of all available files.

pxget

signature(object = "PXDataset", list, force = FALSE, destdir = getwd(), ...): downloads the files from the ProteomeXchange repository. If list is missing, the file to be downloaded can be selected from a menu. If list = "all", all files are downloaded. The file names, as returned by pxfiles can also be used. Alternatively, a logical or numeric indices can be used. All files will be downloaded into the directory specified by destdir (default is the current working directory). Unless force is set to TRUE, files are not downloaded if already present in the destdir directory. Additional parameters can be passed to download.file via .... Invisibly returns the names of the downloaded files.

On Windows, the error

In download.file(urls[i], toget[i], ...) :
    InternetOpenUrl failed: 'The login request was denied'
      

had been reported when downloading files. In such cases, the method argument to download.file can be set. If libcurl is available (try capailities("libcurl") to check this), using pxget(..., method = "libcurl") has proven successful. See ?download.file for more details.

pxid

signature(object = "PXDataset"): returns the unique ProteomeXchange identifier.

pxref

signature(object = "PXDataset"): returns the reference associcated with the object.

pxtax

signature(object = "PXDataset"): returns the scientic taxonomic name of object.

pxurl

signature(object = "PXDataset": returns the base url on the ProteomeXchange server where pxfiles(object) reside.

show

signature(object = "PXDataset"): textual representation of object.

Author(s)

Laurent Gatto

References

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.

Source repository for the ProteomeXchange project: https://code.google.com/p/proteomexchange/

Examples

px <- PXDataset("PXD000001")
px
pxtax(px)
pxurl(px)
pxref(px)
pxfiles(px)
fnm <- pxget(px, "PXD000001_mztab.txt")
library("MSnbase")
readMzTabData(fnm, "PEP")
unlink("PXD000001_mztab.txt")