_pkgdown.yml

url: https://maialab.org/quincunx

home:
  title: Access the PGS Catalog from R
  description: An R package to query, download and wrangle PGS Catalog data.

template:
  bootstrap: 5
  params:
    docsearch:
      api_key: 6eb557c1e1320049dc93c778f9efe639
      index_name: quincunx

articles:
- title: PGS Catalog Concepts
  navbar: PGS Catalog Concepts
  contents:
  - identifiers
  - pgs-construction-process
  - cohorts-samples-sample-sets
- title: Getting PGS Catalog Data
  navbar: Getting PGS Catalog Data
  contents:
  - getting-pgs-scores
  - getting-pgs-publications
  - getting-pgs-sample-sets
  - getting-pgs-performance-metrics
  - getting-traits
  - getting-cohorts
  - getting-releases
  - pgs-scoring-file
- title: Wrangling PGS Catalog Data
  navbar: Wrangling PGS Catalog Data
  contents:
  - pgs-cat-ent-subsetting
- title: Case Studies
  navbar: Case Studies
  contents:
  - risk-strat-brs-patients
  - pgs-scores-mavaddat
- title: More info
  contents:
  - quincunx-s-advantages
  - quincunx-development

reference:
- title: "Get PGS Catalog Data"
  desc: "Receive data from the PGS Catalog REST API."
  contents:
  - get_scores
  - read_scoring_file
  - get_publications
  - get_performance_metrics
  - get_sample_sets
  - get_traits
  - get_cohorts
  - get_trait_categories
  - get_ancestry_categories
  - get_releases
- title: "PGS Catalog Entities"
  desc: "S4 classes for scores, publications, performance_metrics, sample_sets and traits."
  contents:
  - 'scores-class'
  - '`publications-class`'
  - '`performance_metrics-class`'
  - '`sample_sets-class`'
  - '`traits-class`'
- title: "Other Entities"
  desc: "S4 classes for cohorts, trait_categories and releases."
  contents:
  - '`cohorts-class`'
  - '`trait_categories-class`'
  - '`releases-class`'
- title: "Data Wrangling of PGS Catalog Entities"
  desc: >
    S4 methods for combining and tallying scores,
    publications, performance_metrics, sample_set,
    traits, cohorts, trait_categories and releases.
  contents:
  - 'n'
  - 'bind'
  - 'union'
  - 'intersect'
  - 'setdiff'
  - 'setequal'
- title: "Accession identifier mapping"
  desc: >
    Translate accession identifiers between scores,
    publications, performance_metrics, sample_set,
    traits and GWAS studies.
  contents:
  - pgs_to_pgp
  - pgs_to_pss
  - pgs_to_ppm
  - pgs_to_study
  - study_to_pgs
  - pgp_to_pgs
  - pgp_to_pss
  - pgp_to_ppm
  - pss_to_pgs
  - pss_to_pgp
  - pss_to_ppm
  - ppm_to_pgs
  - ppm_to_pgp
  - ppm_to_pss
- title: "Easily navigate web resources"
  desc: >
    Functions that allow you to quickly browse linked information.
  contents:
  - open_in_pgs_catalog
  - open_in_pubmed
  - open_in_dbsnp
- title: "Export to xlsx"
  desc: >
    Exporting scores, publications,
    performance_metrics, sample_set, traits,
    cohorts, trait_categories and releases to xlsx.
  contents:
  - write_xlsx
- title: "Miscellaneous"
  desc: "Other functions."
  contents:
  - clear_cache
- title: "Datasets"
  desc: "Datasets shipped with quincunx"
  contents:
  - stages
  - ancestry_categories

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://maialab.org/quincunx/reference/figures/cintesis.svg' height=24>"