Description

This dataset involves GWAS Catalog SNPs and their traits mapped to Experimental Factor Ontology. This data is prepared based on https://www.ebi.ac.uk/gwas/api/search/downloads/alternative.

Usage

GWAS2EF <- dRDataLoader(RData = "GWAS2EF")

Value

a sparse Matrix of class "dgCMatrix", with the columns for Experimental Factor Ontology terms and rows for GWAS SNPs.

References

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.

Examples

GWAS2EF <- dRDataLoader(RData='GWAS2EF')

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.eg”, “org.At.egGOBP”, “org.At.egGOCC”, “org.At.egGOMF”, “org.At.egPS”, “org.At.egSF”, “org.At.string”, “org.Ce.eg”, “org.Ce.egGOBP”, “org.Ce.egGOCC”, “org.Ce.egGOMF”, “org.Ce.egPS”, “org.Ce.egSF”, “org.Ce.string”, “org.Da.eg”, “org.Da.egGOBP”, “org.Da.egGOCC”, “org.Da.egGOMF”, “org.Da.egPS”, “org.Da.egSF”, “org.Da.string”, “org.Dm.eg”, “org.Dm.egGOBP”, “org.Dm.egGOCC”, “org.Dm.egGOMF”, “org.Dm.egPS”, “org.Dm.egSF”, “org.Dm.string”, “org.Gg.eg”, “org.Gg.egGOBP”, “org.Gg.egGOCC”, “org.Gg.egGOMF”, “org.Gg.egPS”, “org.Gg.egSF”, “org.Gg.string”, “org.Hs.eg”, “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.eg”, “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.eg”, “org.Rn.egGOBP”, “org.Rn.egGOCC”, “org.Rn.egGOMF”, “org.Rn.egPS”, “org.Rn.egSF”, “CLL”, “org.Rn.string”
GWAS2EF[1:10, 1:33]

Error in eval(expr, envir, enclos): object 'GWAS2EF' not found