retrieveLD: Retrieve SNP pairwise LD from locuscompare database

In dingruofan/xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Retrieve SNP pairwise LD from locuscompare database

Description

Note: This function comes from boxiangliu/locuscomparer. If you used this function, please cite the following paper: https://www.nature.com/articles/s41588-019-0404-0 SNP pairwise lD are calculated based on 1000 Genomes Project Phase 3 version 5. For storage-efficiency, the output will only include SNPs with r2 > 0.2 with the input SNP.

Usage

retrieveLD(chr, snp, population)

Arguments

chr	(string) Chromosome name. e.g. '22'. Notice that the name should not contain 'chr'.
snp	(string) SNP rsID.
population	(string) One of the 5 popuations from 1000 Genomes: 'AFR', 'AMR', 'EAS', 'EUR', and 'SAS'.

Value

A data.frame object.

Examples

ld <- retrieveLD('6', 'rs9349379', 'AFR')

dingruofan/xQTLbiolinks documentation built on Feb. 12, 2025, 4:57 a.m.