retrieveLD

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 &gt; 0.2 with the input SNP.

Enables users-customized data retrieval, processing, analysis, and data visualization of molecular quantitative trait locus and gene expression data from public resources through the application programming interface <https://gtexportal.org/home/api-docs/index.html> of 'GTEx' and <http://www.ebi.ac.uk/eqtl/api> of 'eQTL cagalogue'.

Ruofan Ding

xQTLbiolinks

An R Package for Integrative Analysis of Quantitative Trait
Locus Data of 'xQTL'

Xudong Zou

Yangmei Qin

Gao Wang

Lei Li

retrieveLD function

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

Arguments

Retrieve SNP pairwise LD from locuscompare database — retrieveLD

<dl>

<dt>chr</dt>
<dd>(string) Chromosome name. e.g. '22'. Notice that the name should not contain 'chr'.</dd>


<dt>snp</dt>
<dd>(string) SNP rsID.</dd>


<dt>population</dt>
<dd>(string) One of the 5 popuations from 1000 Genomes: 'AFR', 'AMR', 'EAS', 'EUR', and 'SAS'.</dd>

</dl>

retrieveLD: Retrieve SNP pairwise LD from locuscompare database

Description

Usage

Value

Arguments

Examples