_pkgdown.yml

url: https://lcpilling.github.io/ukbrapR/
template:
  bootstrap: 5
  light-switch: true

authors:
  Luke Pilling:
    href: "https://lcpilling.github.io"

reference:
- title: Export required data
- contents:
  - export_tables
- title: Extract genetic variants
- contents:
  - extract_variants
  - make_imputed_bed
  - make_dragen_bed
  - load_bed
- title: Create polygenic score
- contents:
  - create_pgs
- title: Ascertain diagnoses and determine date first diagnosed
- contents:
  - get_diagnoses
  - get_df
- title: Label UK Biobank data fields
- contents:
  - label_ukb_field
  - label_ukb_fields
- title: Upload/download from RAP/worker storage
- contents:
  - upload_to_rap
  - download_from_rap
- title: Spark
  des:   These functions do not require intermediate files but must be executed in a JupyterLab Spark environment.
- contents:
  - get_rap_phenos
  - get_selfrep_illness_spark
  - get_emr_spark

articles:
- title: Get started
  navbar: ~
  contents:
  - ascertain_diagnoses
  - label_fields
  - spark_functions

- title: Upcoming functions
  desc: Ideas for functions or those in development
  contents:
  - extract_fields