Linkage Disequilibrium (LD) of GWAS Catalog SNPs according to the 1000 Genomics Project data (phase 3)


This dataset involves LD of GWAS Catalog SNPs calculated by PLINK based on the 1000 Genomics Project data (phase 3).


GWAS_LD <- dRDataLoader(RData = "GWAS_LD")


a list of sparse Matrix of class "dgCMatrix". Each list represents one of 26 populations and 5 super populations, containing sparse matrix of GWAS Catalog SNPs (rows) and LD SNPs (columns). Non-zero values indicate r2 (only those no less than 0.8). The population include 5 super populations ("AFR", "AMR", "EAS", "EUR", "SAS") and 26 populations ("ACB", "ASW", "BEB", "CDX", "CEU", "CHB", "CHS", "CLM", "ESN", "FIN", "GBR", "GIH", "GWD", "IBS", "ITU", "JPT", "KHV", "LWK", "MSL", "MXL", "PEL", "PJL", "PUR", "STU", "TSI", "YRI"). Explanations for population code can be found at


Malone et al. (2010) Modeling sample variables with an Experimental Factor Ontology. Bioinformatics, 26(8):1112-8.

Welter et al. (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res, 42(Database issue):D1001-6.


GWAS_LD <- dRDataLoader(RData='GWAS_LD')
Error in match.arg(RData): 'arg' should be one of “NA”, “TCGA_mutations”, “ig.DO”, “ig.GOBP”, “ig.GOCC”, “ig.GOMF”, “ig.HPCM”, “ig.HPMA”, “ig.HPMI”, “ig.HPPA”, “ig.MP”, “”, “org.At.egGOBP”, “org.At.egGOCC”, “org.At.egGOMF”, “org.At.egPS”, “org.At.egSF”, “org.At.string”, “”, “org.Ce.egGOBP”, “org.Ce.egGOCC”, “org.Ce.egGOMF”, “org.Ce.egPS”, “org.Ce.egSF”, “org.Ce.string”, “”, “org.Da.egGOBP”, “org.Da.egGOCC”, “org.Da.egGOMF”, “org.Da.egPS”, “org.Da.egSF”, “org.Da.string”, “”, “org.Dm.egGOBP”, “org.Dm.egGOCC”, “org.Dm.egGOMF”, “org.Dm.egPS”, “org.Dm.egSF”, “org.Dm.string”, “”, “org.Gg.egGOBP”, “org.Gg.egGOCC”, “org.Gg.egGOMF”, “org.Gg.egPS”, “org.Gg.egSF”, “org.Gg.string”, “”, “org.Hs.egDGIdb”, “org.Hs.egDO”, “org.Hs.egGOBP”, “org.Hs.egGOCC”, “org.Hs.egGOMF”, “org.Hs.egHPCM”, “org.Hs.egHPMA”, “org.Hs.egHPMI”, “org.Hs.egHPPA”, “org.Hs.egMP”, “org.Hs.egMsigdbC1”, “org.Hs.egMsigdbC2BIOCARTA”, “org.Hs.egMsigdbC2CGP”, “org.Hs.egMsigdbC2CP”, “org.Hs.egMsigdbC2KEGG”, “org.Hs.egMsigdbC2REACTOME”, “org.Hs.egMsigdbC3MIR”, “org.Hs.egMsigdbC3TFT”, “org.Hs.egMsigdbC4CGN”, “org.Hs.egMsigdbC4CM”, “org.Hs.egMsigdbC5BP”, “org.Hs.egMsigdbC5CC”, “org.Hs.egMsigdbC5MF”, “org.Hs.egMsigdbC6”, “org.Hs.egMsigdbC7”, “org.Hs.egMsigdbH”, “org.Hs.egPS”, “org.Hs.egSF”, “org.Hs.string”, “”, “org.Mm.egDO”, “org.Mm.egGOBP”, “org.Mm.egGOCC”, “org.Mm.egGOMF”, “org.Mm.egHPCM”, “org.Mm.egHPMA”, “org.Mm.egHPMI”, “org.Mm.egHPPA”, “org.Mm.egMP”, “org.Mm.egPS”, “org.Mm.egSF”, “org.Mm.string”, “”, “org.Rn.egGOBP”, “org.Rn.egGOCC”, “org.Rn.egGOMF”, “org.Rn.egPS”, “org.Rn.egSF”, “CLL”, “org.Rn.string”
Error in eval(expr, envir, enclos): object 'GWAS_LD' not found
# view the few first data for Great British population (GBR) GWAS_LD$GBR[1:50,1:30]
Error in eval(expr, envir, enclos): object 'GWAS_LD' not found