LDlinkR: An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations

Genomic research involving human genetics and evolutionary biology relies heavily on linkage disequilibrium (LD) to investigate population-specific genetic structure, functionally map regions of disease susceptibility and uncover evolutionary history. Interactive and powerful tools are needed to cal...

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Vydáno v:Frontiers in genetics Ročník 11; s. 157
Hlavní autoři: Myers, Timothy A., Chanock, Stephen J., Machiela, Mitchell J.
Médium: Journal Article
Jazyk:angličtina
Vydáno: Switzerland Frontiers Media S.A 28.02.2020
Témata:
bioinformatics
Genetics
LDlink
linkage disequilibrium
population genetics
population genetics
R
LDlink
bioinformatics
linkage disequilibrium
ISSN:1664-8021, 1664-8021
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Shrnutí:Genomic research involving human genetics and evolutionary biology relies heavily on linkage disequilibrium (LD) to investigate population-specific genetic structure, functionally map regions of disease susceptibility and uncover evolutionary history. Interactive and powerful tools are needed to calculate population-specific LD estimates for integrative genomics research. LDlink is an interactive suite of web-based tools developed to query germline variants in 1000 Genomes Project population groups of interest and generate interactive tables and plots of LD estimates. As an expansion to this resource, we have developed an R package, , designed to rapidly calculate statistics for large lists of variants and LD attributes that eliminates the time needed to perform repetitive requests from the web-based LDlink tool. accelerates genomic research by providing efficient and user-friendly functions to programmatically interrogate and download pairwise LD estimates from expansive lists of genetic variants. is a free and publicly available R package that can be installed from the Comprehensive R Archive Network (CRAN) or downloaded from https://github.com/CBIIT/LDlinkR.
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Edited by: Robert Friedman, University of South Carolina, United States
This article was submitted to Bioinformatics and Computational Biology, a section of the journal Frontiers in Genetics
Reviewed by: Patricio Ricardo Munoz, University of Florida, United States; Marcio Resende, University of Florida, United States
ISSN:1664-8021
1664-8021
DOI:10.3389/fgene.2020.00157