_pkgdown.yml

reference:
- title: UKB Dataframe
  desc: >
    Functions to wrangle the UKB data into a dataframe with meaningful column
    names.
  contents:
  - '`ukb_df`'
  - '`ukb_df_field`'
  - '`ukb_df_full_join`'
  - '`ukb_df_duplicated_name`'
  - '`ukb_centre`'
  - '`ukb_context`'

- title: Genetic Metadata
  desc: >
    Functions to query the associated genetic sample QC information
  contents:
  - '`ukb_gen_read_fam`'
  - '`ukb_gen_read_sample`'
  - '`ukb_gen_rel_count`'
  - '`ukb_gen_related_with_data`'
  - '`ukb_gen_samples_to_remove`'
  - '`ukb_gen_sqc_names`'
  - '`ukb_gen_write_bgenie`'
  - '`ukb_gen_write_plink`'

- title: Disease Diagnoses
  desc: >
    Functions to query the UKB hospital episodes statistics.
  contents:
  - '`ukb_icd_code_meaning`'
  - '`ukb_icd_diagnosis`'
  - '`ukb_icd_freq_by`'
  - '`ukb_icd_keyword`'
  - '`ukb_icd_prevalence`'

- title : Datasets
  desc: ~
  contents:
  - '`ukbcentre`'
  - '`icd10chapters`'
  - '`icd10codes`'
  - '`icd9chapters`'
  - '`icd9codes`'

- title: Defunct
  desc: >
    The genetic metadata functions were written to retrieve genetic metadata
    from the phenotype file for the interim genotype release. The fields
    retrieved became obselete when the full genotyping results were released at
    the end of 2017.

    With the release of the full sample (500K individuals) genotypes, sample QC
    (ukb_sqc_v2.txt) and relatedness (ukbA_rel_sP.txt) data are now supplied as
    separate files. The contents of these files, along with all other genetic
    files are described in UKB Resource 531.
  contents:
  - '`ukb_defunct`'
  - '`ukb_gen_excl`'
  - '`ukb_gen_excl_to_na`'
  - '`ukb_gen_het`'
  - '`ukb_gen_meta`'
  - '`ukb_gen_pcs`'
  - '`ukb_gen_rel`'
  - '`ukb_gen_write_plink_excl`'