_pkgdown.yml

title: "GenomicSuperignature"
type: inverse

reference:
  - title: Classes
    desc: Exported classes
    contents:
      - GenomicSignatures-class
      - PCAGenomicSignatures-class
  - title: Constructors
    desc: Build objects with designated constructor functions
    contents:
      - PCAGenomicSignatures
  - title: Methods and Accessors
    desc: Discover content within PCAGenomicSignatures
    contents:
      - GenomicSignatures-methods
      - PCAGenomicSignatures-methods
  - title: Model Building
    desc: Functions for PCAGenomicSignatures model building
    contents:
      - buildAvgLoading
      - findStudiesInCluster
      - PCinRAV
      - rmNaInf
  - title: Model Application
    desc: Functions for applying PCAGenomicSignatures model to a new data
    contents:
      - calculateScore
      - getModel
      - validate
  - title: Extract Output and Metadata
    contents:
      - annotatePC
      - annotateRAV
      - availableRAVmodel
      - extractPC
      - findKeywordInRAV
      - findSignature
      - findStudiesInCluster
      - getRAVInfo
      - getStudyInfo
      - meshTable
      - subsetEnrichedPathways
      - validatedSignatures
  - title: Visualization
    contents:
      - drawWordcloud
      - heatmapTable
      - plotAnnotatedPCA
      - plotValidate
      - sampleScoreHeatmap
  - title: Misc. Package Docs
    desc: Other package information and data
    contents:
      - droplist
      - filterList
      - miniAllZ
      - miniRAVmodel
      - miniTCGA
      - res_hcut

navbar:
  title: ~
  type: default
  left:
    - text: Reference
      href: reference/index.html
    - text: Vignettes
      menu:
      - text: Quick Start Guide
        href: articles/Quickstart.html
      - text: Model Contents
        href: articles/Contents.html
  right:
  - icon: fa-github fa-lg
    href: /~https://github.com/shbrief/GenomicSuperSignature