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Integrating omics datasets with the OmicsPLS package.

Said El Bouhaddani1,2, Hae-Won Uh3, Geurt Jongbloed4

  • 1Dept. of Biomedical Data Sciences, LUMC, Albinusdreef 2, Leiden, 2300 RC, The Netherlands. s.el_bouhaddani@lumc.nl.

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|October 13, 2018
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Summary
This summary is machine-generated.

OmicsPLS is a new R package providing open-source Two-way Orthogonal Partial Least Squares (O2PLS) for biomedical data integration. This tool efficiently handles diverse datasets and offers visualization, improving accuracy and speed for omics data analysis.

Keywords:
Data-specific variationJoint principal componentsO2PLSOmics data integrationR package

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Area of Science:

  • Biostatistics
  • Bioinformatics
  • Computational Biology

Background:

  • Exponential growth in biomedical data necessitates advanced integration methods.
  • Existing methods struggle with diverse data characteristics, requiring quantification of data-specific variation.
  • Two-way Orthogonal Partial Least Squares (O2PLS) is a proposed method for this task, but lacks open-source software.

Purpose of the Study:

  • To introduce OmicsPLS, a free and open-source R package implementing the O2PLS method.
  • To facilitate the application and development of O2PLS for statistical data integration.
  • To provide efficient handling of both low- and high-dimensional omics datasets.

Main Methods:

  • Developed OmicsPLS as an R package for O2PLS implementation.
  • Included generic methods for inspecting and visualizing O2PLS results.
  • Implemented standard and faster cross-validation methods for component selection.

Main Results:

  • OmicsPLS efficiently handles low- and high-dimensional datasets.
  • A simulation study demonstrated OmicsPLS's superior accuracy and CPU runtime compared to alternatives.
  • The package was successfully demonstrated by integrating genetic and glycomic data.

Conclusions:

  • OmicsPLS offers a free, open-source R package for O2PLS-based statistical data integration.
  • The package is available on CRAN and easily installable in R.
  • OmicsPLS addresses the need for accessible O2PLS software in biomedical research.