retrieveLD: Retrieve SNP pairwise LD from locuscompare database
In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'
retrieveLD R Documentation
Retrieve SNP pairwise LD from locuscompare database
Description
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')
xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.
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| retrieveLD | R Documentation |
Retrieve SNP pairwise LD from locuscompare database
Description
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')
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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