mixOmics: An R package for 'omics feature selection and multiple data integration

PLoS Comput Biol. 2017 Nov 3;13(11):e1005752. doi: 10.1371/journal.pcbi.1005752. eCollection 2017 Nov.

Abstract

The advent of high throughput technologies has led to a wealth of publicly available 'omics data coming from different sources, such as transcriptomics, proteomics, metabolomics. Combining such large-scale biological data sets can lead to the discovery of important biological insights, provided that relevant information can be extracted in a holistic manner. Current statistical approaches have been focusing on identifying small subsets of molecules (a 'molecular signature') to explain or predict biological conditions, but mainly for a single type of 'omics. In addition, commonly used methods are univariate and consider each biological feature independently. We introduce mixOmics, an R package dedicated to the multivariate analysis of biological data sets with a specific focus on data exploration, dimension reduction and visualisation. By adopting a systems biology approach, the toolkit provides a wide range of methods that statistically integrate several data sets at once to probe relationships between heterogeneous 'omics data sets. Our recent methods extend Projection to Latent Structure (PLS) models for discriminant analysis, for data integration across multiple 'omics data or across independent studies, and for the identification of molecular signatures. We illustrate our latest mixOmics integrative frameworks for the multivariate analyses of 'omics data available from the package.

MeSH terms

  • Computational Biology / methods*
  • Data Interpretation, Statistical
  • Genomics*
  • Humans
  • Metabolomics*
  • Neoplasms / genetics
  • Neoplasms / metabolism
  • Software*
  • Systems Biology

Grant support

FR was supported, in part, by the Australian Cancer Research Foundation (ACRF) for the Diamantina Individualised Oncology Care Centre at The University of Queensland Diamantina Institute. KALC was supported, in part, by the National Health and Medical Research Council (NHMRC) Career Development fellowship (APP1087415). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.