An S4 class to represent a set of GWAS Catalog associations

The association object consists of six slots, each a table (tibble), that combined form a relational database of a subset of GWAS Catalog associations. Each association is an observation (row) in the associations table --- main table. All tables have the column association_id as primary key.

Slots

associations

A tibble listing associations. Columns:

association_id: GWAS Catalog association accession identifier, e.g., "20250".
pvalue: Reported p-value for strongest variant risk or effect allele.
pvalue_description: Information describing context of p-value.
pvalue_mantissa: Mantissa of p-value.
pvalue_exponent: Exponent of p-value.
multiple_snp_haplotype: Whether the association is for a multi-SNP haplotype.
snp_interaction: Whether the association is for a SNP-SNP interaction.
snp_type: Whether the SNP has previously been reported. Either 'known' or 'novel'.
risk_frequency: Reported risk/effect allele frequency associated with strongest SNP in controls.
standard_error: Standard error of the effect size.
range: Reported 95% confidence interval associated with strongest SNP risk allele, along with unit in the case of beta coefficients. If 95% CIs have not been not reported, these are estimated using the standard error, when available.
or_per_copy_number: Reported odds ratio (OR) associated with strongest SNP risk allele. Note that all ORs included in the Catalog are >1.
beta_number: Beta coefficient associated with strongest SNP risk allele.
beta_unit: Beta coefficient unit.
beta_direction: Beta coefficient direction, either 'decrease' or 'increase'.
beta_description: Additional beta coefficient comment.
last_mapping_date: Last time this association was mapped to Ensembl.
last_update_date: Last time this association was updated.

loci

A tibble listing loci. Columns:

association_id: GWAS Catalog association accession identifier, e.g., "20250".
locus_id: A locus identifier referring to a single variant locus or to a multi-loci entity such as a multi-SNP haplotype.
haplotype_snp_count: Number of variants per locus. Most loci are single-SNP loci, i.e., there is a one to one relationship between a variant and a locus_id (haplotype_snp_count == NA). There are however cases of associations involving multiple loci at once, such as SNP-SNP interactions and multi-SNP haplotypes. This is signalled in the columns: multiple_snp_haplotype and snp_interaction with value TRUE.
description: Description of the locus identifier, e.g., 'Single variant', SNP x SNP interaction, or 3-SNP Haplotype.

risk_alleles

A tibble listing risk alleles. Columns:

association_id: GWAS Catalog association accession identifier, e.g., "20250".
locus_id: A locus identifier referring to a single variant locus or to a multi-loci entity such as a multi-SNP haplotype.
variant_id: Variant identifier, e.g., 'rs1333048'.
risk_allele: Risk allele or effect allele.
risk_frequency: Reported risk/effect allele frequency associated with strongest SNP in controls (if not available among all controls, among the control group with the largest sample size). If the associated locus is a haplotype the haplotype frequency will be extracted.
genome_wide: Whether this variant allele has been part of a genome-wide study or not.
limited_list: Undocumented.

genes

A tibble listing author reported genes. Columns:

association_id: GWAS Catalog association accession identifier, e.g., "20250".
locus_id: A locus identifier referring to a single variant locus or to a multi-loci entity such as a multi-SNP haplotype.
gene_name: Gene symbol according to HUGO Gene Nomenclature (HGNC).

ensembl_ids

A tibble listing Ensembl gene identifiers. Columns:

association_id: GWAS Catalog association accession identifier, e.g., "20250".
locus_id: A locus identifier referring to a single variant locus or to a multi-loci entity such as a multi-SNP haplotype.
gene_name: Gene symbol according to HUGO Gene Nomenclature (HGNC).
ensembl_id: The Ensembl identifier of an Ensembl gene, see Section Gene annotation in Ensembl for more information.

entrez_ids

A tibble listing Entrez gene identifiers. Columns:

association_id: GWAS Catalog association accession identifier, e.g., "20250".
locus_id: A locus identifier referring to a single variant locus or to a multi-loci entity such as a multi-SNP haplotype.
gene_name: Gene symbol according to HUGO Gene Nomenclature (HGNC).
entrez_id: The Entrez identifier of a gene, see ref. doi:10.1093/nar/gkq1237 for more information.