_pkgdown.yml

url: https://rmagno.eu/gwasrapidd/
template:
  bootstrap: 5
reference:
- title: GWAS Catalog Entities
  desc: S4 classes for studies, associations, variants and traits
  contents:
  - '`studies-class`'
  - '`associations-class`'
  - '`variants-class`'
  - '`traits-class`'
- title: Get GWAS Catalog Entities
  desc: Receive data from the GWAS Catalog REST API.
  contents:
  - get_studies
  - get_associations
  - get_variants
  - get_traits
  - get_metadata
- title: Subset GWAS Catalog Entities
  desc: Extract specific observations from studies, associations, variants or traits.
  contents:
  - '`subset-studies`'
  - '`subset-associations`'
  - '`subset-variants`'
  - '`subset-traits`'
- title: Data Wrangling of GWAS Catalog Entities
  desc: |
    S4 methods for combining and tallying studies, associations, variants and traits.
  contents:
  - 'n'
  - bind
  - union
  - intersect
  - setdiff
  - setequal
- title: Accession identifier mapping
  desc: |
    Translate accession identifiers between studies, associations, variants and traits.
  contents:
  - study_to_association
  - study_to_variant
  - study_to_trait
  - association_to_study
  - association_to_variant
  - association_to_trait
  - variant_to_study
  - variant_to_association
  - variant_to_trait
  - trait_to_study
  - trait_to_association
  - trait_to_variant
- title: Get data outside of GWAS Catalog
  desc: Functions to provide easy access to other web resources.
  contents: get_child_efo
- title: Easily navigate web resources
  desc: Functions that allow you to quickly browse linked information.
  contents:
  - open_in_pubmed
  - open_in_dbsnp
  - open_in_gtex
  - open_in_gwas_catalog
- title: Check functions
  desc: Test and diagnose common impediments.
  contents:
  - is_ebi_reachable
  - exists_variant
- title: Datasets
  desc: Datasets shipped with gwasrapidd
  contents:
  - cytogenetic_bands
  - gc_examples
- title: Miscellaneous
  desc: Other functions
  contents:
  - '`%>%`'
  - write_xlsx
authors:
  Ramiro Magno:
    href: https://rmagno.eu/
  Isabel Duarte:
    href: http://iduarte.eu/
  Ana Teresa Maia:
    href: https://www.linkedin.com/in/ana-teresa-maia-2a1a866/
  CINTESIS:
    href: https://cintesis.eu/
    html: <img src='https://rmagno.eu/gwasrapidd/reference/figures/cintesis.svg' height=24>
  Pattern Institute:
    href: https://www.pattern.institute
    html: <img src='https://rmagno.eu/gwasrapidd/reference/figures/pi.svg' height=24>