snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions
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...
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Published in | Bioinformatics Vol. 34; no. 23; pp. 4112 - 4114 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Oxford University Press
01.12.2018
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Subjects | |
Online Access | Get full text |
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Summary: | 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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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 The authors wish it to be known that, in their opinion, the Kari Nousiainen and Kartiek Kanduri authors should be regarded as Joint First Authors. |
ISSN: | 1367-4803 1460-2059 1367-4811 |
DOI: | 10.1093/bioinformatics/bty460 |