_pkgdown.yaml

title: pathwayPCA
url: https://gabrielodom.github.io/pathwayPCA/
template:
  params:
    bootswatch: united

authors:
  Gabriel Odom:
    href: https://github.com/gabrielodom
  Lily Wang:
    href: http://biostat.med.miami.edu/people/primary-faculty/lily-wang-ph.d
  Steven Chen:
    href: http://biostat.med.miami.edu/people/primary-faculty/xi-steven-chen-ph.d

navbar:
  components:
    home: ~
    articles:
      text: User Guides
      menu:
      - text: Integrative Pathway Analysis with pathwayPCA
        href: articles/Introduction_to_pathwayPCA.html
      - text: -------
      - text: "Supplemental Material"
      - text: Quick-start Guide
        href: articles/Supplement1-Quickstart_Guide.html
      - text: Import and Tidy Data
        href: articles/Supplement2-Importing_Data.html
      - text: Creating -Omics Data Objects
        href: articles/Supplement3-Create_Omics_Objects.html
      - text: Pathway-PCA Methods
        href: articles/Supplement4-Methods_Walkthrough.html
      - text: Result Visualization Guide
        href: articles/Supplement5-Analyse_Results.html
    news:
      text: Version Logs
      href: news/index.html

reference:
  - title: Pathway Collections
    desc: Functions to create or modify pathway collection objects
    contents:
      - '`read_gmt`'
      - '`write_gmt`'
      - '`CreatePathwayCollection`'
      - '`print.pathwayCollection`'
      - '`SubsetPathwayCollection`'
  - title: Creating S4-Class Objects and Basic Methods
    desc: Descriptions, creators, and accessors of the Omics* S4 classes
    contents:
      - '`OmicsPathway-class`'
      - '`OmicsSurv-class`'
      - '`OmicsReg-class`'
      - '`OmicsCateg-class`'
      - '`ValidOmicsSurv`'
      - '`TransposeAssay`'
      - '`SE2Tidy`'
      - '`CreateOmics`'
      - '`show,OmicsPathway-method`'
      - '`getAssay`'
      - '`getAssay<-`'
      - '`getPathwayCollection`'
      - '`getPathwayCollection<-`'
      - '`getSampleIDs`'
      - '`getSampleIDs<-`'
      - '`getEventTime`'
      - '`getEventTime<-`'
      - '`getEvent`'
      - '`getEvent<-`'
      - '`getResponse`'
      - '`getResponse<-`'
  - title: PCA-method Functions
    desc: Functions to analyze Omics-class objects
    contents:
      - '`pathwayPCA-package`'
      - '`AESPCA_pVals`'
      - '`SuperPCA_pVals`'
      - '`SubsetPathwayData`'
      - '`getPathPCLs`'
      - '`getPathpVals`'
      - '`LoadOntoPCs`'
  - title: Example Data Sets
    desc: Data for function examples
    contents:
      - '`colon_pathwayCollection`'
      - '`colonSurv_df`'
      - '`wikipwsHS_Entrez_pathwayCollection`'
  - title: Internal AES-PCA Functions
    desc: Functions designed to be called by the AES-PCA wrapper above
    contents:
      - '`aespca`'
      - '`lars.lsa`'
      - '`ExtractAESPCs`'
      - '`PermTestSurv`'
      - '`PermTestReg`'
      - '`PermTestCateg`'
      - '`normalize`'
  - title: Internal Supervised PCA Functions
    desc: Functions designed to be called by the Supervised PCA wrapper above
    contents:
      - '`coxTrain_fun`'
      - '`olsTrain_fun`'
      - '`glmTrain_fun`'
      - '`superpc.st`'
      - '`superpc.train`'
      - '`mysvd`'
      - '`OptimGumbelMixParams`'
      - '`GumbelMixpValues`'
      - '`pathway_tControl`'
      - '`pathway_tScores`'
  - title: Internal Supplemental Functions
    desc: Utility functions shared by both the AES-PCA and supervised PCA methods or CreateOmics
    contents:
      - '`CreateOmicsPath`'
      - '`CreateOmicsSurv`'
      - '`CreateOmicsReg`'
      - '`CreateOmicsCateg`'
      - '`IntersectOmicsPwyCollct`'
      - '`TabulatepValues`'
      - '`ControlFDR`'
      - '`RandomControlSample`'