title: MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration.
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.
authors.affiliation: Institut de Salut Global de Barcelona (ISGlobal) - Campus Mar, Barcelona Biulding: Biomedical Research Park, c/Dr. Aiguader, 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.|CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Hernandez-Ferrer
authors.affiliation: Institut de Salut Global de Barcelona (ISGlobal) - Campus Mar, Barcelona Biulding: Biomedical Research Park, c/Dr. Aiguader, 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.|CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Ruiz-Arenas
authors.affiliation: Institut de Salut Global de Barcelona (ISGlobal) - Campus Mar, Barcelona Biulding: Biomedical Research Park, c/Dr. Aiguader, 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.|CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
authors.forename: Alba
authors.initials: A
authors.lastname: Beltran-Gomila
authors.affiliation: Institut de Salut Global de Barcelona (ISGlobal) - Campus Mar, Barcelona Biulding: Biomedical Research Park, c/Dr. Aiguader, 88, 08003, Barcelona, Spain. juanr.gonzalez@isglobal.org.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. juanr.gonzalez@isglobal.org.|CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain. juanr.gonzalez@isglobal.org.
authors.forename: Juan R
authors.initials: JR
authors.lastname: González
mesh_terms: D019175:DNA Methylation; D015870:Gene Expression; D023281:Genomics / Q000379:methods*; D006801:Humans; D015999:Multivariate Analysis; D012984:Software
keywords: Data infrastructure; Data integration; Data organization; Omics data; R