PXDataset2 {rpx}R Documentation

New PXDataset (v2) to find and download proteomics data

Description

The rpx package provides the infrastructure to access, store and retrieve information for ProteomeXchange (PX) data sets. This can be achieved with PXDataset2 objects can be created with the PXDataset2() constructor that takes the unique ProteomeXchange project identifier as input.

The new PXDataset2 class superseeds the previous and now deprecated PXDataset version.

Usage

PXDataset2(id, cache = rpxCache())

PXDataset(id, cache = rpxCache())

## S4 method for signature 'PXDataset2'
pxid(object)

## S4 method for signature 'PXDataset2'
pxurl(object)

## S4 method for signature 'PXDataset2'
pxtax(object)

## S4 method for signature 'PXDataset2'
pxref(object)

pxtitle(object)

## S4 method for signature 'PXDataset2'
pxfiles(object, n = 10)

## S4 method for signature 'PXDataset2'
pxCacheInfo(object)

## S4 method for signature 'PXDataset2'
pxget(object, list, cache = rpxCache())

Arguments

id

character(1) containing a valid ProteomeXchange identifier.

cache

Object of class BiocFileCache. Default is to use the central rpx cache returned by rpxCache(), but users can use their own cache. See rpxCache() for details.

object

An instance of class PXDataset2.

n

integer(1) indicating the number of files to be printed.

list

character(), numeric() or logical() defining the project files to be downloaded. This list of files can retrieved with pxfiles().

Details

The rpx packages uses caching to store ProteomeXchange projects and project files. When creating an object with PXDataset2(), the cache is first queried for the projects identifier. If a unique hit is found, the project is retrieved and returned. If no matching project identifier is found, then the remote resource is accessed to first create the new PXDataset2() project, then cache it before returning it to the user. The same mechanism is applied when project files are requested.

Caching is supported by BiocFileCache package. The PXDataset2() constructor and the px_get() function can be passed a instance of class BiocFileCache that defines the cache. The default is to use the package-wide cache defined in rpxCache(). For more details on how to manage the cache (for example if some files need to be deleted), please refer to the BiocFileCache package vignette and documentation. See also rpxCache() for additional details.

Value

The PXDataset2() returns a cached PXDataset2 object. It thus also modifies the cache used to projet caching, as defined by the cache argument.

Slots

px_id

character(1) containing the dataset's unique ProteomeXchange identifier, as used to create the object.

px_rid

character(1) storing the cached resource name in the BiocFileCache instance stored in cachepath.

px_title

character(1) with the project's title.

px_url

‘character(1) with the project’s URL.

px_doi

character(1) with the project's DOI.

px_ref

character containing the project's reference(s).

px_ref_doi

character containing the project's reference DOIs.

px_pubmed

character containing the project's reference PubMed identifier.

px_files

data.frame containing information about the project files, including file names, URIs and types. The files are retrieved from the project's README.txt file.

px_tax

charcter (typically of length 1) containing the taxonomy of the sample.

px_metadata

list containing the project's metadata, as downloaded from the ProteomeXchange site. All slots but px_files are populated from this one.

cachepath

character(1) storing the path to the cache the project object is stored in.

Accessors

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 <- PXDataset2("PXD000001")
px
pxtax(px)
pxurl(px)
pxref(px)
pxfiles(px)
pxCacheInfo(px)

fas <- pxget(px, "erwinia_carotovora.fasta")
fas
library("Biostrings")
readAAStringSet(fas)

[Package rpx version 2.0.3 Index]