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iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database
BACKGROUND: The iRefIndex addresses the need to consolidate protein interaction data into a single uniform data resource. iRefR provides the user with access to this data source from an R environment. RESULTS: The iRefR package includes tools for selecting specific subsets of interest from the iRefI...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282787/ https://www.ncbi.nlm.nih.gov/pubmed/22115179 http://dx.doi.org/10.1186/1471-2105-12-455 |
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author | Mora, Antonio Donaldson, Ian M |
author_facet | Mora, Antonio Donaldson, Ian M |
author_sort | Mora, Antonio |
collection | PubMed |
description | BACKGROUND: The iRefIndex addresses the need to consolidate protein interaction data into a single uniform data resource. iRefR provides the user with access to this data source from an R environment. RESULTS: The iRefR package includes tools for selecting specific subsets of interest from the iRefIndex by criteria such as organism, source database, experimental method, protein accessions and publication identifier. Data may be converted between three representations (MITAB, edgeList and graph) for use with other R packages such as igraph, graph and RBGL. The user may choose between different methods for resolving redundancies in interaction data and how n-ary data is represented. In addition, we describe a function to identify binary interaction records that possibly represent protein complexes. We show that the user choice of data selection, redundancy resolution and n-ary data representation all have an impact on graphical analysis. CONCLUSIONS: The package allows the user to control how these issues are dealt with and communicate them via an R-script written using the iRefR package - this will facilitate communication of methods, reproducibility of network analyses and further modification and comparison of methods by researchers. |
format | Online Article Text |
id | pubmed-3282787 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-32827872012-02-21 iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database Mora, Antonio Donaldson, Ian M BMC Bioinformatics Research Article BACKGROUND: The iRefIndex addresses the need to consolidate protein interaction data into a single uniform data resource. iRefR provides the user with access to this data source from an R environment. RESULTS: The iRefR package includes tools for selecting specific subsets of interest from the iRefIndex by criteria such as organism, source database, experimental method, protein accessions and publication identifier. Data may be converted between three representations (MITAB, edgeList and graph) for use with other R packages such as igraph, graph and RBGL. The user may choose between different methods for resolving redundancies in interaction data and how n-ary data is represented. In addition, we describe a function to identify binary interaction records that possibly represent protein complexes. We show that the user choice of data selection, redundancy resolution and n-ary data representation all have an impact on graphical analysis. CONCLUSIONS: The package allows the user to control how these issues are dealt with and communicate them via an R-script written using the iRefR package - this will facilitate communication of methods, reproducibility of network analyses and further modification and comparison of methods by researchers. BioMed Central 2011-11-24 /pmc/articles/PMC3282787/ /pubmed/22115179 http://dx.doi.org/10.1186/1471-2105-12-455 Text en Copyright ©2011 Mora and Donaldson; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Mora, Antonio Donaldson, Ian M iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database |
title | iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database |
title_full | iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database |
title_fullStr | iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database |
title_full_unstemmed | iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database |
title_short | iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database |
title_sort | irefr: an r package to manipulate the irefindex consolidated protein interaction database |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282787/ https://www.ncbi.nlm.nih.gov/pubmed/22115179 http://dx.doi.org/10.1186/1471-2105-12-455 |
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