studies-class: An S4 class to represent a set of GWAS Catalog studies
In ramiromagno/gwasrapidd: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

studies-class

R Documentation

An S4 class to represent a set of GWAS Catalog studies

Description

The studies object consists of eight slots, each a table (tibble), that combined form a relational database of a subset of GWAS Catalog studies. Each study is an observation (row) in the studies table — main table. All tables have the column study_id as primary key.

Slots

studies

study_id: GWAS Catalog study accession identifier, e.g., "GCST002735".
reported_trait: Phenotypic trait as reported by the authors of the study, e.g. "Breast cancer".
initial_sample_size: Free text description of the initial cohort sample size.
replication_sample_size: Free text description of the replication cohort sample size.
gxe: Whether the study investigates a gene-environment interaction.
gxg: Whether the study investigates a gene-gene interaction.
snp_count: Number of variants passing quality control.
qualifier: Qualifier of number of variants passing quality control.
imputed: Whether variants were imputed.
pooled: Whether samples were pooled.
study_design_comment: Any other relevant study design information.
full_pvalue_set: Whether full summary statistics are available for this study.
user_requested: Whether the addition of this study to the GWAS Catalog was requested by a user.

genotyping_techs

A tibble listing genotyping technologies employed in each study. Columns:

study_id: GWAS Catalog study accession identifier.
genotyping_technology: Genotyping technology employed, e.g. "Exome genotyping array", "Exome-wide sequencing", "Genome-wide genotyping array", "Genome-wide sequencing", or "Targeted genotyping array".

platforms

A tibble listing platforms used per study.

study_id: GWAS Catalog study accession identifier.
manufacturer: Platform manufacturer, e.g., "Affymetrix", "Illumina", or "Perlegen".

ancestries

A tibble listing ancestry of samples used in each study.

study_id: GWAS Catalog study accession identifier.
ancestry_id: Ancestry identifier.
type: Stage of the ancestry sample: either 'initial' or 'replication'.
number_of_individuals: Number of individuals comprising this ancestry sample.

ancestral_groups

A tibble listing ancestral groups used in each ancestry.

study_id: GWAS Catalog study accession identifier.
ancestry_id: Ancestry identifier.
ancestral_group: Genetic ancestry groups present in the sample.

countries_of_origin

A tibble listing countries of origin of samples.

study_id: GWAS Catalog study accession identifier.
ancestry_id: Ancestry identifier.
country_name: Country name, according to The United Nations M49 Standard of Geographic Regions.
major_area: Region name, according to The United Nations M49 Standard of Geographic Regions.
region: Sub-region name, according to The United Nations M49 Standard of Geographic Regions.

countries_of_recruitment

A tibble listing countries of recruitment of samples.

study_id: GWAS Catalog study accession identifier.
ancestry_id: Ancestry identifier.
country_name: Country name, according to The United Nations M49 Standard of Geographic Regions.
major_area: Region name, according to The United Nations M49 Standard of Geographic Regions.
region: Sub-region name, according to The United Nations M49 Standard of Geographic Regions.

publications

A tibble listing publications associated with each study.

study_id: GWAS Catalog study accession identifier.
pubmed_id: PubMed identifier.
publication_date: Publication date (online date if available) formatted as ymd.
publication: Abbreviated journal name.
title: Publication title.
author_fullname: Last name and initials of first author.
author_orcid: Author's ORCID iD (Open Researcher and Contributor ID).