MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
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- dc.contributor.author Hernandez-Ferrer, Carles, 1987-ca
- dc.contributor.author Ruiz-Arenas, Carlosca
- dc.contributor.author Beltran-Gomila, Albaca
- dc.contributor.author González Ruiz, Juan Ramónca
- dc.date.accessioned 2018-06-27T08:08:08Z
- dc.date.available 2018-06-27T08:08:08Z
- dc.date.issued 2017
- dc.description.abstract 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.
- dc.description.sponsorship 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)
- dc.format.mimetype application/pdf
- dc.identifier.citation Hernandez-Ferrer C, Ruiz-Arenas C, Beltran-Gomila A, González JR. MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. BMC Bioinformatics. 2017 Jan 17; 18(1): 36. DOI: 10.1186/s12859-016-1455-1
- dc.identifier.doi http://dx.doi.org/10.1186/s12859-016-1455-1
- dc.identifier.issn 1471-2105
- dc.identifier.uri http://hdl.handle.net/10230/34978
- dc.language.iso eng
- dc.publisher BioMed Centralca
- dc.relation.ispartof BMC Bioinformatics. 2017 Jan 17;18(1):36
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/308333
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/MTM2015-68140-R
- dc.rights © 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/)
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.other Genòmica
- dc.subject.other Programari
- dc.title MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integrationca
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion