Journal
BIOINFORMATICS
Volume 31, Issue 2, Pages 273-274Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu622
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Funding
- National Institutes of Health (NIH-)NCI [P30 CA006973]
- Cleveland Foundation The Helen Masenhimer Fellowship Award
- NIH-NCRR [UL1 RR 025005]
- NIH-NCI [K25 CA141053]
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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.
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