A1 Refereed original research article in a scientific journal
snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions
Authors: Kari Nousiainen, Kartiek Kanduri, Isis Ricaño-Ponce, Cisca Wijmenga, Riitta Lahesmaa, Vinod Kumar, Harri Lähdesmäki
Publication year: 2018
Journal: Bioinformatics
Article number: bty460
Volume: 34
Issue: 23
First page : 4112
Last page: 4114
Number of pages: 3
ISSN: 1367-4803
eISSN: 1460-2059
DOI: https://doi.org/10.1093/bioinformatics/bty460
Web address : https://academic.oup.com/bioinformatics/article/34/23/4112/5034433
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/33334184
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.
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.
The software is available at https://github.com/kartiek/snpEnrichR.
Downloadable publication This is an electronic reprint of the original article. |  |
