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Genome Med. 2014 Oct 14;6(10):79. doi: 10.1186/s13073-014-0079-1. eCollection 2014.

SuRFing the genomics wave: an R package for prioritising SNPs by functionality.

Author information

1
Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK.
2
Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK ; Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ UK.
3
MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK.

Abstract

Identifying functional non-coding variants is one of the greatest unmet challenges in genetics. To help address this, we introduce an R package, SuRFR, which integrates functional annotation and prior biological knowledge to prioritise candidate functional variants. SuRFR is publicly available, modular, flexible, fast, and simple to use. We demonstrate that SuRFR performs with high sensitivity and specificity and provide a widely applicable and scalable benchmarking dataset for model training and validation. Website: http://www.cgem.ed.ac.uk/resources/.

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