_pkgdown.yml

destination: docs
template:
  params:
    bootswatch: flatly
reference:
  - title: "Prior to TWAS"
    desc: >
      Functions for file formatting and eQTL analysis
    contents:
      - convertToDosage
      - eQTL_MOSTWAS
      - mergeFinalModels
  - title: "MOSTWAS modeling"
    desc: >
      Main wrapper functions for MOSTWAS expression models
    contents:
      - trainLocalModel
      - MeTWAS
      - DePMA
  - title: "Association testing"
    desc: >
      Functions for TWAS association testing
    contents:
      - burdenTest
      - addedLastTest
  - title: "Simulation framework"
    desc: >
      Functions for running simulation analysis
    contents:
      - regress
      - simBeta
      - simEQTL
      - simGeno
      - simGWAS
      - simTrait
  - title: "Miscellaneous"
    desc: >
      Functions used internally in MOSTWAS
    contents:
      - adjR2
      - amplifyTrans
      - computeTME
      - CVFitMediator
      - estimateHeritability
      - gatherMediators
      - getCisGenotypes
      - LDprune
      - permuteTME
      - RepParallel
      - sobelTest
      - testTME
      - trainMediator
      - trainSNPPheno
      - trainDeP
      - trainExpression