_pkgdown.yaml

title: coloc
url: https://chr1swallace.github.io/coloc
template:
  params:
    bootswatch: simplex
news:
articles:
- title: Vignettes
  navbar: ~
  contents:
  - a01_intro
  - a02_data
  - a03_enumeration
  - a04_sensitivity
  - a06_SuSiE
  - a05_conditioning
reference:
  - title: Coloc data structure
    desc: Description of coloc data structure
    contents:
      - '`check_dataset`'
  - title: Bayesian enumeration of hypotheses
    desc: Two trait colocalisation and single trait fine mapping under
      single causal variant assumptions
    contents:
      - '`coloc.abf`'
      - '`finemap.abf`'
  - title: Sensitivity analysis
    desc: Check how robust inference is to changing prior parameter values
    contents:
      - '`sensitivity`'
  - title: Relaxing the single variant assumption
    desc: use conditioning or masking to account for multiple independent causal variants per trait
    contents:
      - '`coloc.susie`'
      - '`runsusie`'
  - title: Others
    desc: included for completeness, but the main functions you need should be in the sections above
    contents:
      - '`Var.data`'
      - '`Var.data.cc`'
      - '`approx.bf.estimates`'
      - '`approx.bf.p`'
      - '`bin2lin`'
      - '`check_alignment`'
      - '`coloc-package`'
      - '`coloc.bf_bf`'
      - '`coloc.detail`'
      - '`coloc.process`'
      - '`coloc.signals`'
      - '`coloc.susie_bf`'
      - '`coloc_test_data`'
      - '`combine.abf`'
      - '`est_cond`'
      - '`estgeno.1.ctl`'
      - '`find.best.signal`'
      - '`findends`'
      - '`findpeaks`'
      - '`finemap.bf`'
      - '`finemap.signals`'
      - '`logbf_to_pp`'
      - '`logdiff`'
      - '`logsum`'
      - '`map_cond`'
      - '`map_mask`'
      - '`plot.coloc_abf`'
      - '`plot_dataset`'
      - '`print.coloc_abf`'
      - '`process.dataset`'
      - '`sdY.est`'
      - '`subset_dataset`'