functions/_pkgdown.yml at main · mattlee821/functions · GitHub

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url: ~
template:
  bootstrap: 5

navbar:
  components:
    articles:
      text: Articles
      menu:
        - text: Getting Started
          href: articles/getting-started.html
        - text: Mendelian Randomization Workflow
          href: articles/mr-workflow.html
        - text: Colocalisation Analysis
          href: articles/colocalisation.html
        - text: Visualisation
          href: articles/visualisation.html

articles:
- title: Common Workflows
  contents:
  - getting-started
  - mr-workflow
  - colocalisation
  - visualisation

reference:
- title: Mendelian Randomization
  desc: Functions for MR data formatting, harmonization, and analysis.
  contents:
  - format_data
  - mr_leaveoneout_plot
  - mr_density_plot
  - mr_funnel_plot
  - mr_forest_plot
  - mr_scatter_plot
  - calculate_r2
  - calculate_fstat_from_r2
  - calculate_fstat_from_beta_se
  - directional_consistency
  - alignment_check

- title: Colocalization
  desc: Utilities for colocalization analysis and sensitivity checks.
  contents:
  - coloc_check_alignment
  - coloc_sensitivity
  - coloc_prior.adjust
  - coloc_prior.snp2hyp
  - coloc_manh.plot
  - coloc_plot_dataset
  - finemap_pval_LD
  - finimom_cs_table
  - susieR_cs_table

- title: Visualization
  desc: Plotting functions for GWAS results and regional associations.
  contents:
  - manhattan
  - qqplot
  - miamiplot
  - gg_regionplot
  - gg_locusplot
  - forestplot
  - blank_plot
  - calculate_and_insert_percent_change

- title: LocusComparer Integration
  desc: Utilities for integrating with the locuscomparer package.
  contents:
  - locuscomparer

- title: Utilities & Variant Search
  desc: General purpose functions and variant search utilities.
  contents:
  - read_file
  - remove_duplicate_SNP
  - remove_nearby_positions
  - biomaRt_getBM_batch
  - get_ld_proxies
  - proxy_search
  - proxy_search_DECODE
  - proxy_search_UKB
  - proxy_search_split
  - missing_EAF
  - replace_na_with_mean
  - model_test
  - palette
  - create_ids
  - random_string