MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
BACKGROUND: Reduction in the cost of genomic assays has generated large amounts of biomedical-related data. As a result, current studies perform multiple experiments in the same subjects. While Bioconductor's methods and classes implemented in different packages manage individual experiment...
| Autores: | , , , |
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| Formato: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2017 |
| País: | España |
| Recursos: | Universitat Pompeu Fabra |
| Repositorio: | Repositorio Digital de la UPF |
| OAI Identifier: | oai:repositori.upf.edu:10230/34978 |
| Acesso em linha: | http://hdl.handle.net/10230/34978 http://dx.doi.org/10.1186/s12859-016-1455-1 |
| Access Level: | acceso abierto |
| Palavra-chave: | Genòmica Programari |
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MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integrationHernandez-Ferrer, Carles, 1987-Ruiz-Arenas, CarlosBeltran-Gomila, AlbaGonzález Ruiz, Juan RamónGenòmicaProgramariBACKGROUND: Reduction in the cost of genomic assays has generated large amounts of biomedical-related data. As a result, current studies perform multiple experiments in the same subjects. While Bioconductor's methods and classes implemented in different packages manage individual experiments, there is not a standard class to properly manage different omic datasets from the same subjects. In addition, most R/Bioconductor packages that have been designed to integrate and visualize biological data often use basic data structures with no clear general methods, such as subsetting or selecting samples. RESULTS: To cover this need, we have developed MultiDataSet, a new R class based on Bioconductor standards, designed to encapsulate multiple data sets. MultiDataSet deals with the usual difficulties of managing multiple and non-complete data sets while offering a simple and general way of subsetting features and selecting samples. We illustrate the use of MultiDataSet in three common situations: 1) performing integration analysis with third party packages; 2) creating new methods and functions for omic data integration; 3) encapsulating new unimplemented data from any biological experiment.CONCLUSIONS: MultiDataSet is a suitable class for data integration under R and Bioconductor framework.This work has been partly funded by the Spanish Ministry of Economy and Competitiveness (MTM2015-68140-R). CH-F was supported by a grant from European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no 308333 – the HELIX project. CR-A was supported by a FI fellowship from Catalan Government (#016FI_B 00272)BioMed Central201820182017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/34978http://dx.doi.org/10.1186/s12859-016-1455-1reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésBMC Bioinformatics. 2017 Jan 17;18(1):36info:eu-repo/grantAgreement/EC/FP7/308333info:eu-repo/grantAgreement/ES/1PE/MTM2015-68140-R© Carles Hernandez-Ferrer, Carlos Ruiz-Arenas, Alba Beltran-Gomila, Juan R. González. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/349782026-06-12T07:21:37Z |
| dc.title.none.fl_str_mv |
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration |
| title |
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration |
| spellingShingle |
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration Hernandez-Ferrer, Carles, 1987- Genòmica Programari |
| title_short |
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration |
| title_full |
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration |
| title_fullStr |
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration |
| title_full_unstemmed |
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration |
| title_sort |
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration |
| dc.creator.none.fl_str_mv |
Hernandez-Ferrer, Carles, 1987- Ruiz-Arenas, Carlos Beltran-Gomila, Alba González Ruiz, Juan Ramón |
| author |
Hernandez-Ferrer, Carles, 1987- |
| author_facet |
Hernandez-Ferrer, Carles, 1987- Ruiz-Arenas, Carlos Beltran-Gomila, Alba González Ruiz, Juan Ramón |
| author_role |
author |
| author2 |
Ruiz-Arenas, Carlos Beltran-Gomila, Alba González Ruiz, Juan Ramón |
| author2_role |
author author author |
| dc.subject.none.fl_str_mv |
Genòmica Programari |
| topic |
Genòmica Programari |
| description |
BACKGROUND: Reduction in the cost of genomic assays has generated large amounts of biomedical-related data. As a result, current studies perform multiple experiments in the same subjects. While Bioconductor's methods and classes implemented in different packages manage individual experiments, there is not a standard class to properly manage different omic datasets from the same subjects. In addition, most R/Bioconductor packages that have been designed to integrate and visualize biological data often use basic data structures with no clear general methods, such as subsetting or selecting samples. RESULTS: To cover this need, we have developed MultiDataSet, a new R class based on Bioconductor standards, designed to encapsulate multiple data sets. MultiDataSet deals with the usual difficulties of managing multiple and non-complete data sets while offering a simple and general way of subsetting features and selecting samples. We illustrate the use of MultiDataSet in three common situations: 1) performing integration analysis with third party packages; 2) creating new methods and functions for omic data integration; 3) encapsulating new unimplemented data from any biological experiment.CONCLUSIONS: MultiDataSet is a suitable class for data integration under R and Bioconductor framework. |
| publishDate |
2017 |
| dc.date.none.fl_str_mv |
2017 2018 2018 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10230/34978 http://dx.doi.org/10.1186/s12859-016-1455-1 |
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http://hdl.handle.net/10230/34978 http://dx.doi.org/10.1186/s12859-016-1455-1 |
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Inglés |
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Inglés |
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BMC Bioinformatics. 2017 Jan 17;18(1):36 info:eu-repo/grantAgreement/EC/FP7/308333 info:eu-repo/grantAgreement/ES/1PE/MTM2015-68140-R |
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http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf application/pdf |
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BioMed Central |
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BioMed Central |
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reponame:Repositorio Digital de la UPF instname:Universitat Pompeu Fabra |
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