_pkgdown.yml

url: https://cemordaunt.github.io/comethyl/
template:
  bootstrap: 5
authors:
  sidebar:
    roles: [cre, aut, ctb]
navbar:
  structure:
    left:  [intro, reference, article1, article2, article3]
    right: [search, github]
  components:
    article1:
      text: CpG Cluster Analysis
      href: articles/CpG_Cluster_Analysis.html
    article2:
      text: Gene Body Analysis
      href: articles/Gene_Body_Analysis.html
    article3:
      text: Module Preservation
      href: articles/Module_Preservation.html
home:
  sidebar:
    structure: [links, license, community, custom, authors, dev]
    components:
      custom:
        title: Citation
        text: Comethyl [Publication](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab554/6509051)
reference:
- title: Package
  contents:
  - comethyl
- title: Prepare Methylation Data
  contents:
  - adjustRegionMeth
  - filterCpGs
  - filterRegions
  - getCpGs
  - getCpGtotals
  - getDendro
  - getPCs
  - getRegionMeth
  - getRegionTotals
  - getRegions
  - plotCpGtotals
  - plotDendro
  - plotRegionStats
  - plotRegionTotals
  - plotSDstats
- title: Construct Network
  contents:
  - getCor
  - getModuleBED
  - getModules
  - getSoftPower
  - plotHeatmap
  - plotRegionDendro
  - plotSoftPower
- title: Explore Modules
  contents:
  - annotateModule
  - enrichModule
  - getGeneList
  - getMEtraitCor
  - listOntologies
  - plotEnrichment
  - plotMEtraitCor
  - plotMEtraitDot
  - plotMEtraitScatter
  - plotMethTrait
- title: Test Module Preservation
  contents:
  - getModulePreservation
  - plotModulePreservation