_pkgdown.yml

url: https://nicksunderland.github.io/genepi.utils/
template:
  bootstrap: 5
  light-switch: true

reference:
- title: "GWAS standardisation"
  desc: >
    Functions for standardising GWAS inputs
  contents:
  - GWAS
  - ColumnMap
  - Column
  # - standardise_gwas
  # - harmonise_gwases
  # - ColumnMapping
  # - format_gwas_output
  - lift
  - as.data.table
  # - get_map
  # - input_formats
  # - is.input_format

- title: "GWAS processing"
  desc: >
    Functions for prosessing GWAS data
  contents:
  - clump
  - harmonise_gwas
  - ld_matrix
  - get_pfile_variants
  - get_proxies
  - subset_gwas
  # - download_ukbb_ld

- title: "Mendelian Randomization"
  desc: >
    Functions for performing MR
  contents:
  - MR
  - reset_index_snp
  - clump_mr
  - mr_egger
  - mr_ivw
  - mr_pcgmm
  - mr_results_to_data_table
  - mr_weighted_median
  - mr_weighted_mode
  - run_mr
  - plot_mr
  - set_ld_mat
  - to_MRInput
  - to_MRMVInput
  - ld_matrix
  # - download_ukbb_ld

- title: "RSID mapping"
  desc: >
    Functions for mapping chromosome and position data to variant RSIDs
  contents:
  - chrpos_to_rsid

- title: "Collider bias"
  desc: >
    Functions for analysing collider / index event bias and adjust GWAS data for this bias.
  contents:
  - collider_bias
  - cwls
  - slopehunter
  - dudbridge

- title: "Plotting"
  desc: >
    Functions for creating common GenEpi data plots
  contents:
  - manhattan
  - miami
  - qq_plot
  - eaf_plot
  - generate_random_gwas_data
  - plot_coloc_probabilities

- title: "Setup"
  desc: >
    Functions for package configuration
  contents:
  - set_dbsnp_directory
  - which_dbsnp_builds
  - which_dbsnp_directory
  - set_1000G_reference
  - set_plink2
  - which_1000G_reference
  - which_plink2