switchBox: an R package for k-Top Scoring Pairs classifier development

Bioinformatics. 2015 Jan 15;31(2):273-4. doi: 10.1093/bioinformatics/btu622. Epub 2014 Sep 26.


k-Top Scoring Pairs (kTSP) is a classification method for prediction from high-throughput data based on a set of the paired measurements. Each of the two possible orderings of a pair of measurements (e.g. a reversal in the expression of two genes) is associated with one of two classes. The kTSP prediction rule is the aggregation of voting among such individual two-feature decision rules based on order switching. kTSP, like its predecessor, Top Scoring Pair (TSP), is a parameter-free classifier relying only on ranking of a small subset of features, rendering it robust to noise and potentially easy to interpret in biological terms. In contrast to TSP, kTSP has comparable accuracy to standard genomics classification techniques, including Support Vector Machines and Prediction Analysis for Microarrays. Here, we describe 'switchBox', an R package for kTSP-based prediction.

Availability: The 'switchBox' package is freely available from Bioconductor: http://www.bioconductor.org.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Biomarkers, Tumor / genetics*
  • Breast Neoplasms / classification*
  • Breast Neoplasms / genetics
  • Computational Biology / methods*
  • Female
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Neoplasm Recurrence, Local / diagnosis*
  • Neoplasm Recurrence, Local / genetics
  • Support Vector Machine


  • Biomarkers, Tumor