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. 2016 Jan 15;32(2):289-91.
doi: 10.1093/bioinformatics/btv562. Epub 2015 Sep 30.

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests

Bernat Gel  1 , Anna Díez-Villanueva  1 , Eduard Serra  1 , Marcus Buschbeck  2 , Miguel A Peinado  1 , Roberto Malinverni  3
Affiliations

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests

Bernat Gel et al. Bioinformatics. .

Abstract

Motivation: Statistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model.

Summary: regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association.

Availability and implementation: regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR).

Contact: rmalinverni@carrerasresearch.org.

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Figures

Fig. 1.
Fig. 1.
(A) Plot of the results of a permutation test assessing the association between a subset of 1000 HepG2 CTCF narrow peaks (ENCODE/Broad Institute) and CpG islands (Wu et al., 2010), using a per chromosome randomization of CTCF peaks, the number of overlaps as the evaluation function and 5000 permutations. The association is highly significant with the observed value far from the limit of significance of the random distribution. (B) Plot of the local z-score of the permutation test in A. The association is strongly related to the exact position of the CTCF peaks since the z-score drops sharply as soon as the regions are shifted a few hundreds of bases
See this image and copyright information in PMC

References

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