multiclassPairs: an R package to train multiclass pair-based classifier

MOTIVATION: k–Top Scoring Pairs (kTSP) algorithms utilize in-sample gene expression feature pair rules for class prediction, and have demonstrated excellent performance and robustness. The available packages and tools primarily focus on binary prediction (i.e. two classes). However, many real-world classification problems e.g. tumor subtype prediction, are multiclass tasks. RESULTS: Here, we present multiclassPairs, an R package to train pair-based single sample classifiers for multiclass problems. multiclassPairs offers two main methods to build multiclass prediction models, either using a one-versus-rest kTSP scheme or through a novel pair-based Random Forest approach. The package also provides options for dealing with class imbalances, multiplatform training, missing features in test data and visualization of training and test results. AVAILABILITY AND IMPLEMENTATION: ‘multiclassPairs’ package is available on CRAN servers and GitHub: https://github.com/NourMarzouka/multiclassPairs. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.