Integrating omics datasets with the OmicsPLS package
Authors/Creators
- 1. Dept. of Biomedical Data Sciences, LUMC, Albinusdreef 2, Leiden, 2300 RC, The Netherlands
- 2. Department of Biostatistics and Research Support, UMC Utrecht, div. Julius Centre, Huispost Str. 6.131, Utrecht, 3508 GA, The Netherlands
- 3. Delft Institute of Applied Mathematics, EEMCS, TU Delft, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
- 4. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
- 5. Genos Glycobiology Laboratory, Zagreb, 10000, Croatia
- 6. Dept. of Statistics, University of Leeds, Leeds, LS2 9JT, United Kingdom
Description
Background: With the exponential growth in available biomedical data, there is a need for data integration methods that can extract information about relationships between the data sets. However, these data sets might have very different characteristics. For interpretable results, data-specific variation needs to be quantified. For this task, Two-way Orthogonal Partial Least Squares (O2PLS) has been proposed. To facilitate application and development of the methodology, free and open-source software is required. However, this is not the case with O2PLS.
Results: We introduce OmicsPLS, an open-source implementation of the O2PLS method in R. It can handle both low- and high-dimensional datasets efficiently. Generic methods for inspecting and visualizing results are implemented. Both a standard and faster alternative cross-validation methods are available to determine the number of components. A simulation study shows good performance of OmicsPLS compared to alternatives, in terms of accuracy and CPU runtime. We demonstrate OmicsPLS by integrating genetic and glycomic data.
Conclusions: We propose the OmicsPLS R package: a free and open-source implementation of O2PLS for statistical data integration. OmicsPLS is available at https://cran.r-project.org/package=OmicsPLS and can be installed in R via install.packages("OmicsPLS").