MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration

BMC Bioinformatics

Software

Alba Beltran-Gomila¹  Juan R. González¹  Carlos Ruiz-Arenas¹  Carles Hernandez-Ferrer¹ 

[1] 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;

关键词: Omics data;    Data integration;    Data infrastructure;    Data organization;    R;   

DOI  :  10.1186/s12859-016-1455-1

 received in 2016-06-11, accepted in 2016-12-24,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundReduction 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.ResultsTo 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.ConclusionsMultiDataSet is a suitable class for data integration under R and Bioconductor framework.

【 授权许可】

CC BY   
© The Author(s). 2017