retrieve_LD: Retrive SNP pairwise LD from database. SNP pairwise lD are...
In boxiangliu/locuscomparer: locuscomparer: Visualization of GWAS-QTL Colocalization Events
retrieve_LD R Documentation
Retrive SNP pairwise LD from database.
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.
Description
Retrive SNP pairwise LD from database.
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
retrieve_LD(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'.
Examples
retrieve_LD('6', 'rs9349379', 'AFR')
boxiangliu/locuscomparer documentation built on Nov. 27, 2022, 7:26 a.m.
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| retrieve_LD | R Documentation |
Retrive SNP pairwise LD from database. 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.
Description
Retrive SNP pairwise LD from database. 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
retrieve_LD(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'. |
Examples
retrieve_LD('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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