An S4 class to represent a set of GWAS Catalog variantsSource:
The variants object consists of four slots, each a table
tibble), that combined form a relational database of a
subset of GWAS Catalog variants. Each variant is an observation (row) in the
variants table --- main table. All tables have the column
variant_id as primary key.
tibblelisting variants. Columns:
Variant identifier, e.g.,
Whether this SNP has been merged with another SNP in a newer genome build.
Class according to Ensembl's predicted consequences that each variant allele may have on transcripts. See Ensembl Variation - Calculated variant consequences.
Last time this variant was updated.
tibblelisting genomic contexts associated with each variant. Columns:
Gene symbol according to HUGO Gene Nomenclature (HGNC).
Genomic distance between the variant and the gene (in base pairs).
Whether this is a mapped gene to this variant. A mapped gene is either an overlapping gene with the variant or the two closest genes upstream and downstream of the variant. Moreover, only genes whose mapping source is 'Ensembl' are considered.
Whether this is the closest gene to this variant.
Whether this variant is intergenic, i.e, if there is no gene up or downstream within 100kb.
Whether this variant is upstream of this gene.
Whether this variant is downstream of this gene.
Gene mapping source, either
Gene mapping method.
tibblelisting gene Ensembl identifiers associated with each genomic context. Columns:
tibblelisting gene Entrez identifiers associated with each genomic context. Columns: