RankAggreg, an R package for weighted rank aggregation
Open Access
- 19 February 2009
- journal article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 10 (1), 62
- https://doi.org/10.1186/1471-2105-10-62
Abstract
Background: Researchers in the field of bioinformatics often face a challenge of combining several ordered lists in a proper and efficient manner. Rank aggregation techniques offer a general and flexible framework that allows one to objectively perform the necessary aggregation. With the rapid growth of high-throughput genomic and proteomic studies, the potential utility of rank aggregation in the context of meta-analysis becomes even more apparent. One of the major strengths of rank-based aggregation is the ability to combine lists coming from different sources and platforms, for example different microarray chips, which may or may not be directly comparable otherwise. Results: The RankAggreg package provides two methods for combining the ordered lists: the Cross-Entropy method and the Genetic Algorithm. Two examples of rank aggregation using the package are given in the manuscript: one in the context of clustering based on gene expression, and the other one in the context of meta-analysis of prostate cancer microarray experiments. Conclusion: The two examples described in the manuscript clearly show the utility of the RankAggreg package in the current bioinformatics context where ordered lists are routinely produced as a result of modern high-throughput technologies.Keywords
This publication has 9 references indexed in Scilit:
- Integration of Ranked Lists via Cross Entropy Monte Carlo with Applications to mRNA and microRNA StudiesBiometrics, 2009
- Finding common genes in multiple cancer types through meta–analysis of microarray experiments: A rank aggregation approachGenomics, 2008
- Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approachBioinformatics, 2007
- Inhibition of fatty acid synthase activity in prostate cancer cells by dutasterideThe Prostate, 2007
- Variants in the HEPSIN gene are associated with prostate cancer in men of European originHuman Genetics, 2006
- Combining Results of Microarray Experiments: A Rank Aggregation ApproachStatistical Applications in Genetics and Molecular Biology, 2006
- A Tutorial on the Cross-Entropy MethodAnnals of Operations Research, 2005
- α-Methylacyl Coenzyme A Racemase as a Tissue Biomarker for Prostate CancerJAMA, 2002
- The Cross-Entropy Method for Combinatorial and Continuous OptimizationMethodology and Computing in Applied Probability, 1999