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Merged
danielnachun merged 1 commit into from
Jun 30, 2026
Merged

fix website #538

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28 changes: 26 additions & 2 deletions _pkgdown.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,9 @@ reference:
- LdEigen-class
- LdScore-class
- LdStatistic-class
- MashPrior-class
- MultiStudyQtlDataset-class
- SldscData-class
- SumStatsBase-class

- title: "Class constructors"
Expand All @@ -111,10 +113,12 @@ reference:
- GwasFineMappingResult
- GwasSumStats
- LdData
- MashPrior
- MultiStudyQtlDataset
- QtlDataset
- QtlFineMappingResult
- QtlSumStats
- SldscData
- TwasWeights
- TwasWeightsEntry

Expand Down Expand Up @@ -226,6 +230,7 @@ reference:

- subtitle: "QtlDataset"
contents:
- getAf
- getGenotypeCovariates
- getGenotypes
- getPhenotypeCovariates
Expand All @@ -248,9 +253,23 @@ reference:
- getQcInfo
- getQcDiagnostics

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

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

- subtitle: "TwasWeights"
contents:
- getCvPerformance
- getCvResult
- getDataType
- getFits
- getStandardized
Expand All @@ -260,7 +279,7 @@ reference:
- subtitle: "TwasWeightsEntry"
contents:
# Same generic surface as TwasWeights — dispatches on per-row entries.
- getCvPerformance
- getCvResult
- getDataType
- getFits
- getStandardized
Expand Down Expand Up @@ -313,6 +332,7 @@ reference:
- autoDecision
- raiss
- mergeVariantInfo
- mergeSusieCs
- parseCsCorr
- filterRelatedness

Expand Down Expand Up @@ -370,6 +390,7 @@ reference:
- susieAshRssWeights
- mvsusieWeights
- mvsusieRssWeights
- fsusieWeights
- fitMvsusie
- fitMvsusieRss
- fitFsusie
Expand Down Expand Up @@ -470,6 +491,8 @@ reference:
- computeSldscMRef
- readAnnotations
- readSldscTrait
- readSldscAnnot
- readSldscFrq
- standardizeSldscTrait
- h2EstimateToSldscTrait
- isBinarySldscAnnot
Expand Down Expand Up @@ -511,6 +534,7 @@ reference:
- enlocPipeline
- ctwasBimfileLoader
- getCtwasMetaData
- mergeCtwasBoundaryRegions
- loadRegionalAssociationData
- loadRegionalUnivariateData
- loadRegionalRegressionData
Expand Down
5 changes: 3 additions & 2 deletions vignettes/twas-weights.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ head(getWeights(entry))
CV performance:

```{r individual-cv}
entry@cvPerformance
getCvResult(entry)
```

The entry's `variantIds` slot lists the LD-aligned variant set the
Expand Down Expand Up @@ -232,7 +232,8 @@ Each entry exposes:
- `weights` — per-variant coefficients (named numeric vector or matrix
for multivariate methods)
- `variantIds` — variant IDs the weights are aligned to
- `cvPerformance` — list with `rsq`, `r`, predicted values, etc.
- `cvResult` — list with `rsq`, `r`, predicted values, etc. (access
with `getCvResult()`)
- `standardized` — whether weights are on the standardized
(`y ~ scale(X)`) or original scale
- `dataType` — string tag carried through for reporting (e.g.
Expand Down
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