RpepXML-package: R interface to the pepXML standard
In RpepXML: R interface to the pepXML standard

Description Details Author(s) References

RpepXML allows to load MSMS pipeline analysis data in pepXML format and provides programmatic access to the different elements. It also allow to filter the identificaiton results based on peptide rank and ion score.

Package:	RpepXML
Type:	Package
Version:	0.1
Date:	2010-08-27
License:	Artitic-2.0
LazyLoad:	yes

From the Trans-Proteomic Pipeline (TPP) pepXML page: ‘pepXML Is an open data format developed at the SPC/Institute for Systems biology for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans. pepXML is intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses.’

Currently, only the msms_pipeline_analysis element and children are implemented. The overall structure is simplified and not all attributes are implemented (yet). The most important elements should be in place to import, manipulate and filter pepXML data.

See the package vignette for details about the package's usage and underlying classes. An dummy example data set tinySearch.pepXML is also provided.

Laurent Gatto Maintainer: Laurent Gatto <lg390@cam.ac.uk>

http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML, http://sashimi.sourceforge.net/schema_revision/pepXML/Docs/pepXML_v18.html.

RpepXML documentation built on May 2, 2019, 5:15 p.m.