RankAggreg, an R package for weighted rank aggregation

• Published in: BMC bioinformatics Vol. 10; no. 1; p. 62
• Main Authors: Pihur, Vasyl, Datta, Susmita, Datta, Somnath
• Format: Journal Article
• Language: English
• Published: London BioMed Central 19.02.2009; BioMed Central Ltd; BMC
• Subjects: Algorithms; Applications software; Bioinformatics; Biomedical and Life Sciences; Cancer; Cluster Analysis; Computational biology; Computational Biology - methods; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Gene Expression Profiling - methods; Genetic algorithms; Genetic aspects; Life Sciences; Microarrays; Oligonucleotide Array Sequence Analysis - methods; Software; United States; Borda Count; Individual List; Genetic Algorithm Algorithm; Rank Aggregation; Brute Force Approach
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-10-62

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.