Multivariate Analysis with the R Package mixOmics

The high-dimensional nature of proteomics data presents challenges for statistical analysis and biological interpretation. Multivariate analysis, combined with insightful visualization can help to reveal the underlying patterns in complex biological data. This chapter introduces the R package mixOmics which focuses on data exploration and integration. We first introduce methods for single data sets: both Principal Component Analysis, which can identify the patterns of variance present in data, and sparse Partial Least Squares Discriminant Analysis, which aims to identify variables that can classify samples into known groups. We then present integrative methods with Projection to Latent Structures and further extensions for discriminant analysis. We illustrate each technique on a breast cancer multi-omics study and provide the R code and data as online supplementary material for readers interested in reproducing these analyses.