snpEnrichR

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Journal Title
Journal ISSN
Volume Title
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Date
2018-12-01
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Mcode
Degree programme
Language
en
Pages
3
4112-4114
Series
Bioinformatics (Oxford, England), Volume 34, issue 23
Abstract
Motivation: Co-localization of trait associated SNPs for specific transcription-factor binding sites or regulatory regions in the genome can yield profound insight into underlying causal mechanisms. Analysis is complicated because the truly causal SNPs are generally unknown and can be either SNPs reported in GWAS studies or other proxy SNPs in their linkage disequilibrium. Hence, a comprehensive pipeline for SNP co-localization analysis that utilizes all relevant information about both the genotyped SNPs and their proxies is needed. Results: We developed an R package snpEnrichR for SNP co-localization analysis. The software integrates different tools for random SNP generation and genome co-localization analysis to automatize and help users to create custom SNP co-localization analysis. We show via an example that including proxy SNPs in SNP co-localization analysis enhances the sensitivity of co-localization detection. Availability and implementation: The software is available at https://github.com/kartiek/snpEnrichR.
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Citation
Nousiainen , K , Kanduri , K , Ricaño-Ponce , I , Wijmenga , C , Lahesmaa , R , Kumar , V & Lähdesmäki , H 2018 , ' snpEnrichR : analyzing co-localization of SNPs and their proxies in genomic regions ' , Bioinformatics (Oxford, England) , vol. 34 , no. 23 , pp. 4112-4114 . https://doi.org/10.1093/bioinformatics/bty460