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Bioinformatics. 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.

Author information

1
Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and.
2
Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and Josep Carreras Institute for Leukaemia Research (IJC), Campus ICO-HGTP, Campus Can Ruti, Badalona, Spain.
3
Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and.

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.

PMID:
26424858
PMCID:
PMC4708104
DOI:
10.1093/bioinformatics/btv562
[Indexed for MEDLINE]
Free PMC Article

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