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Bioinformatics. 2011 Jun 15;27(12):1729-30. doi: 10.1093/bioinformatics/btr233. Epub 2011 Apr 19.

Rgtsp: a generalized top scoring pairs package for class prediction.

Author information

1
Bioinformatics Core Facility, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland. vlad.popovici@isb-sib.ch

Abstract

SUMMARY:

A top scoring pair (TSP) classifier consists of a pair of variables whose relative ordering can be used for accurately predicting the class label of a sample. This classification rule has the advantage of being easily interpretable and more robust against technical variations in data, as those due to different microarray platforms. Here we describe a parallel implementation of this classifier which significantly reduces the training time, and a number of extensions, including a multi-class approach, which has the potential of improving the classification performance.

AVAILABILITY AND IMPLEMENTATION:

Full C++ source code and R package Rgtsp are freely available from http://lausanne.isb-sib.ch/~vpopovic/research/. The implementation relies on existing OpenMP libraries.

PMID:
21505033
DOI:
10.1093/bioinformatics/btr233
[Indexed for MEDLINE]

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