_pkgdown.yml

url: https://statfungen.github.io/pecotmr

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 bootstrap: 5
 light-switch: true
 math-rendering: katex
 bslib:
  base_font: { google: "Roboto" }
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development:
 mode: auto

home:
 links:
 - text: Learn more
   href: https://github.com/StatFunGen/pecotmr
 - text: Report a bug
   href: https://github.com/StatFunGen/pecotmr/issues

navbar:
 structure:
  left: [intro, reference, articles]
  right: [search, github, lightswitch]
 components:
  intro:
   icon: fa fa-play-circle
   text: Get Started
   href: articles/fine-mapping.html
   aria-label: Get started with pecotmr
  reference:
   icon: fa fa-file-code
   text: Functions
   href: reference/index.html
   aria-label: Function reference
  articles:
   icon: fa fa-book-reader
   text: Vignettes
   href: articles/index.html
   aria-label: Articles and vignettes
  github:
   icon: fab fa-github
   href: https://github.com/StatFunGen/pecotmr
   aria-label: View source on GitHub

articles:
  - title: "Quality Control"
    desc: >
      Allele alignment and LD-mismatch QC for GWAS and QTL summary
      statistics.
    contents:
    - rss-qc
  - title: "Fine-mapping"
    desc: >
      SuSiE-family fine-mapping for individual-level QTL data, QTL
      summary statistics, and GWAS summary statistics.
    contents:
    - fine-mapping
  - title: "TWAS"
    desc: >
      Training TWAS weights from QTL data (individual-level and
      summary-statistics, single and multi-context) and computing
      per-gene TWAS Z-scores from GWAS summary statistics.
    contents:
    - twas-weights
    - twas-zscore
  - title: "Colocalization"
    desc: >
      Pairwise QTL/GWAS colocalization (coloc.bf_bf) and multi-trait
      colocalization with ColocBoost.
    contents:
    - coloc-pipeline
    - colocboost-pipeline
  - title: "Enrichment Analysis"
    contents:
    - xqtl-enrichment
  - title: "Resources"
    navbar: ~
    contents:
    - qtl-gwas-resources

reference:
  - title: "Class definitions"
    desc: >
      S4 class definitions. The `-class` topic documents the slots and
      validity constraints; the matching constructor topic (next
      section) documents the user-facing factory function.
    contents:
      - AnnotationMatrix-class
      - FineMappingResultBase-class
      - GenotypeHandle-class
      - H2Estimate-class
      - LdData-class
      - LdEigen-class
      - LdScore-class
      - LdStatistic-class
      - MashPrior-class
      - MultiStudyQtlDataset-class
      - SldscData-class
      - SumStatsBase-class

  - title: "Class constructors"
    desc: >
      User-facing constructors. For classes that have both a `-class`
      topic and a constructor topic, prefer the constructor for
      day-to-day use; the `-class` topic is the authoritative slot
      reference.
    contents:
      - AnnotationMatrix
      - FineMappingEntry
      - GenotypeHandle
      - GwasFineMappingResult
      - GwasSumStats
      - LdData
      - MashPrior
      - MultiStudyQtlDataset
      - QtlDataset
      - QtlFineMappingResult
      - QtlSumStats
      - SldscData
      - TwasWeights
      - TwasWeightsEntry

  - title: "Class methods"
    desc: >
      Accessor and behaviour methods grouped by the class they're
      defined on. Generics with implementations on multiple classes
      appear under each. S4 pipeline dispatch methods
      (`fineMappingPipeline`, `colocboostPipeline`,
      `twasWeightsPipeline`) are listed under "Pipelines" further
      down rather than repeated per class.

  - subtitle: "AnnotationMatrix"
    contents:
      - getAnnotationMeta
      - getAnnotations
      - getBaseline
      - getCandidates
      - getGenome
      - getSnpRanges

  - subtitle: "FineMappingEntry"
    contents:
      - adjustPips
      - getCs
      - getMarginalEffects
      - getPip
      - getSusieFit
      - getTopLoci
      - getVariantIds

  - subtitle: "FineMappingResultBase"
    contents:
      - getLdSketch
      - getMethodNames
      - getStudy
      - writeSumstatsVcf

  - subtitle: "GenotypeHandle"
    contents:
      - getFormat
      - getNSamples
      - getPath
      - getPgenPtr
      - getSampleIds
      - getSnpInfo
      - readGenotypes

  - subtitle: "GwasFineMappingResult"
    contents:
      - getContexts
      - getFineMappingResult
      - getTraits

  - subtitle: "GwasSumStats"
    contents:
      - getMaf
      - getN
      - getSumStats
      - getSumstatDf
      - getVarY
      - getZ
      - nSnps
      - subsetChr

  - subtitle: "H2Estimate"
    contents:
      - getEnrichment
      - getH2
      - getLocal
      - getScoreStats
      - getTauBlocks

  - subtitle: "LdBlocks"
    contents:
      - getBlocks

  - subtitle: "LdData"
    contents:
      - getBlockMetadata
      - getCorrelation
      - getGenotypeHandle
      - getGenotypes
      - getMixtureWeights
      - getNRef
      - getRefPanel
      - getSnpIdx
      - getVariantInfo
      - hasGenotypes

  - subtitle: "LdEigen"
    contents:
      - getEigenList

  - subtitle: "LdScore"
    contents:
      - getLdMatrixList
      - getLdScoreWeights
      - getLdScores

  - subtitle: "LdStatistic"
    contents:
      - getInSample
      - getLdBlocks

  - subtitle: "MultiStudyQtlDataset"
    contents:
      - getQtlDatasets

  - subtitle: "QtlDataset"
    contents:
      - getAf
      - getGenotypeCovariates
      - getGenotypes
      - getPhenotypeCovariates
      - getPhenotypes
      - getResidualizedGenotypes
      - getResidualizedPhenotypes
      - getScaleResiduals

  - subtitle: "QtlFineMappingResult"
    contents:
      - getFineMappingResult

  - subtitle: "QtlSumStats"
    contents:
      - getContexts
      - getTraits

  - subtitle: "SumStatsBase"
    contents:
      - getQcInfo
      - getQcDiagnostics

  - subtitle: "SldscData"
    contents:
      - getAnnotData
      - getFrqData
      - getTraitRuns
      - getTraitNames
      - getAnnotCols
      - getTraitRun

  - subtitle: "MashPrior"
    contents:
      - getCvFits
      - getFullFit

  - subtitle: "TwasWeights"
    contents:
      - getCvResult
      - getDataType
      - getFits
      - getStandardized
      - getTwasWeights
      - getWeights

  - subtitle: "TwasWeightsEntry"
    contents:
      # Same generic surface as TwasWeights — dispatches on per-row entries.
      - getCvResult
      - getDataType
      - getFits
      - getStandardized
      - getVariantIds
      - getWeights

  - title: "Pipelines"
    desc: >
      End-to-end pipeline entry points. Each takes one or more S4
      input classes and returns a SumStats, FineMappingResult,
      TwasWeights collection, or a tabular summary.
    contents:
      - causalInferencePipeline
      - colocboostPipeline
      - colocPipeline
      - ctwasPipeline
      - fineMappingPipeline
      - mashPipeline
      - qtlEnrichmentPipeline
      - sldscPostprocessingPipeline
      - twasWeightsPipeline

  - title: "cTWAS"
    desc: >
      The four chainable steps that `ctwasPipeline` is built from:
      `assembleCtwasInputs` → `estCtwasParam` → `screenCtwasRegions`
      → `finemapCtwasRegions`. Use the steps directly when you want
      to override the estimated priors (e.g. fall back to the prefit
      EM values after an accurate-EM divergence), inspect the assembled
      region data, or run only part of the pipeline.
    contents:
      - assembleCtwasInputs
      - estCtwasParam
      - screenCtwasRegions
      - finemapCtwasRegions

  - title: "Quality control"
    desc: >
      Summary-statistics QC orchestrator plus the underlying allele
      harmonization, LD-mismatch, kriging, SLALOM, DENTIST, RAISS,
      and relatedness checks.
    contents:
      - summaryStatsQc
      - alignVariantNames
      - ldMismatchQc
      - krigingOutlierQc
      - slalom
      - dentist
      - dentistSingleWindow
      - autoDecision
      - raiss
      - mergeVariantInfo
      - mergeSusieCs
      - parseCsCorr
      - filterRelatedness

  - title: "LD infrastructure"
    desc: >
      Loading and manipulating LD matrices, plus design-matrix
      conditioning utilities.
    contents:
      - loadLdMatrix
      - loadLdSketch
      - checkLd
      - enforceDesignFullRank
      - ldClumpByScore
      - ldLoader
      - ldPruneByCorrelation
      - filterVariantsByLdReference

  - title: "Genotype I/O"
    desc: >
      Reading and manipulating per-region genotype data outside the
      GenotypeHandle accessor surface.
    contents:
      - extractBlockGenotypes
      - computeBlockLdCor
      - loadGenotypeRegion
      - readAfreq
      - getRefVariantInfo
      - invertMinmaxScaling

  - title: "Variant ID and region helpers"
    desc: >
      Parsing, formatting, and overlap checks for variant IDs
      (`chr:pos:A2:A1`) and genomic regions (`chr:start-end`).
    contents:
      - parseVariantId
      - normalizeVariantId
      - classifyVariantType
      - regionToDf
      - regionsOverlap
      - findOverlappingRegions

  - title: "Fine-mapping"
    desc: >
      SuSiE-family fit wrappers (individual-level and summary-stat
      variants) plus the shared post-processing that produces the
      unified `top_loci` table. The VCF writer for fine-mapping
      results is documented under
      \code{FineMappingResultBase} in the Class methods section above.
    contents:
      - susieWeights
      - susieRssWeights
      - susieInfWeights
      - susieInfRssWeights
      - susieAshWeights
      - susieAshRssWeights
      - mvsusieWeights
      - mvsusieRssWeights
      - fsusieWeights
      - fitMvsusie
      - fitMvsusieRss
      - fitFsusie
      - fitSusieInfThenSusieRss
      - fsusieGetCs
      - fsusieWrapper
      - getSusieResult
      - buildTopLoci
      - extractCsInfo
      - extractTopPipInfo
      - formatFinemappingOutput
      - lbfToAlpha
      - postprocessFinemappingFits

  - title: "TWAS"
    desc: >
      Per-method weight-training functions invoked by
      `twasWeightsPipeline()`, the cross-validation / ensembling
      machinery that combines them, and multi-method p-value
      combination. Grouped by method family below. (SuSiE-family
      weight functions live under "Fine-mapping" above since they
      double as fine-mappers.)

  - subtitle: "Penalized regression"
    contents:
      - lassosumRss
      - lassosumRssWeights
      - mcpWeights
      - mcpRssWeights
      - scadWeights
      - scadRssWeights
      - l0learnWeights
      - l0learnRssWeights
      - penalizedRss

  - subtitle: "Bayesian alphabet"
    contents:
      - bayesAlphabetWeights
      - bayesAWeights
      - bayesBWeights
      - bayesCWeights
      - bayesLWeights
      - bayesNWeights
      - bayesRWeights
      - bLassoWeights
      - prsCs
      - prsCsWeights
      - sdpr
      - sdprWeights
      - dprWeights

  - subtitle: "mr.mash / mr.ash"
    contents:
      - mrashWeights
      - mrAshRssWeights
      - mrmashWeights
      - mrmashRssWeights
      - mrmashWrapper
      - buildMrmashPriorMatrices
      - computeCovDiag
      - computeCovFlash

  - subtitle: "Ensembling / cross-validation / prediction"
    contents:
      - learnTwasWeights
      - ensembleWeights
      - twasWeightsCv
      - twasPredict
      - twasZ
      - estimateSparsity

  - subtitle: "Multi-method p-value combination"
    contents:
      - combinePValues

  - title: "mash helpers"
    desc: >
      Utilities exposed by the mash track for posterior contrast
      construction, mixture management, and meta-analysis.
    contents:
      - makePairwiseContrastCol
      - fitMashContrast
      - metaAnalysisPerCell
      - sanitizeMashData
      - sliceMashData
      - updateMashModelCov

  - title: "Heritability and enrichment"
    desc: >
      Heritability estimation, LD-score computation, stratified
      LD-score regression utilities, and per-variant QTL/GWAS
      enrichment analysis (low-level kernel that powers
      \code{qtlEnrichmentPipeline}).
    contents:
      - estimateH2
      - computeLdScores
      - computeSldscAnnotSd
      - computeSldscMRef
      - readAnnotations
      - readSldscTrait
      - readSldscAnnot
      - readSldscFrq
      - standardizeSldscTrait
      - h2EstimateToSldscTrait
      - isBinarySldscAnnot
      - metaSldscRandom
      - qtlEnrichment

  - title: "Bundled datasets and example helpers"
    desc: >
      Synthetic data shipped with the package for vignettes and
      tests. `fixupExampleGenotypePaths()` re-points the bundled
      GenotypeHandle paths at the install-time `inst/extdata/`
      location.
    contents:
      - fixupExampleGenotypePaths
      - qtl_dataset_example
      - qtl_sumstats_example
      - qtl_sumstats_multicontext_example
      - gwas_sumstats_s4_example
      - multi_study_qtl_dataset_example
      - eqtl_region_example
      - gwas_sumstats_example
      - gwas_finemapping_example
      - qtl_finemapping_example
      - multitraite_data

  - title: internal
    desc: >
      Deprecated entry points retained for backward compatibility.
      Each emits a `.Deprecated()` warning and forwards to the
      canonical replacement. Hidden from the reference index but
      still searchable and rendered.
    contents:
      - alleleQc
      - matchRefPanel
      - xqtlEnrichmentWrapper
      - computeQtlEnrichment
      - colocWrapper
      - colocPostProcessor
      - enlocPipeline
      - ctwasBimfileLoader
      - getCtwasMetaData
      - mergeCtwasBoundaryRegions
      - loadRegionalAssociationData
      - loadRegionalUnivariateData
      - loadRegionalRegressionData
      - loadRegionalMultivariateData
      - loadRegionalFunctionalData
      - loadTwasWeights
      - loadRssData
      - loadMultitaskRegionalData
      - regionDataToIndInput
      - regionDataToRssInput
      - harmonizeTwas
      - harmonizeGwas
      - loadStudyLd
      - univariateAnalysisPipeline
      - rssAnalysisPipeline
      - multivariateAnalysisPipeline
      - susieRssPipeline
      - twasPipeline
      - twasMultivariateWeightsPipeline
      - standardiseSumstatsColumns
      - loadTsvRegion
      - batchLoadTwasWeights
      - loadMultitraitTensorqtlSumstat
      - loadMultitraitRSumstat
      # Implementation details with .Rd topics but no front-facing role.
      - as.data.frame.GwasSumStats
      - rescaleCovW0
      - "getSumStats,GwasSumStats-method"

footer:
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  left: developed_by
  right: built_with