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dc.contributor Aalto-yliopisto fi
dc.contributor Aalto University en
dc.contributor.author Nousiainen, Kari
dc.contributor.author Kanduri, Kartiek
dc.contributor.author Ricaño-Ponce, Isis
dc.contributor.author Wijmenga, Cisca
dc.contributor.author Lahesmaa, Riitta
dc.contributor.author Kumar, Vinod
dc.contributor.author Lähdesmäki, Harri
dc.date.accessioned 2018-12-21T10:29:47Z
dc.date.available 2018-12-21T10:29:47Z
dc.date.issued 2018-12-01
dc.identifier.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 en
dc.identifier.issn 1367-4803
dc.identifier.issn 1460-2059
dc.identifier.other PURE UUID: 4201805f-9b7a-4bc4-a4b8-705ae25b1f0f
dc.identifier.other PURE ITEMURL: https://research.aalto.fi/en/publications/4201805f-9b7a-4bc4-a4b8-705ae25b1f0f
dc.identifier.other PURE LINK: http://www.scopus.com/inward/record.url?scp=85057185798&partnerID=8YFLogxK
dc.identifier.other PURE FILEURL: https://research.aalto.fi/files/30293227/bty460.pdf
dc.identifier.uri https://aaltodoc.aalto.fi/handle/123456789/35642
dc.description.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. en
dc.format.extent 3
dc.format.extent 4112-4114
dc.format.mimetype application/pdf
dc.language.iso en en
dc.relation.ispartofseries Bioinformatics (Oxford, England) en
dc.relation.ispartofseries Volume 34, issue 23 en
dc.rights openAccess en
dc.title snpEnrichR en
dc.type A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä fi
dc.description.version Peer reviewed en
dc.contributor.department Centre of Excellence in Molecular Systems Immunology and Physiology Research Group, SyMMys
dc.contributor.department Åbo Akademi University
dc.contributor.department University of Groningen
dc.contributor.department Helsinki Institute for Information Technology (HIIT)
dc.contributor.department Department of Computer Science en
dc.identifier.urn URN:NBN:fi:aalto-201812216650
dc.identifier.doi 10.1093/bioinformatics/bty460
dc.type.version publishedVersion

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