From 40b40c7ff3bc122af021a2045635e942c00d5436 Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 29 Jun 2026 17:49:14 -0700
Subject: [PATCH] fix website

---
 _pkgdown.yml               | 28 ++++++++++++++++++++++++++--
 vignettes/twas-weights.Rmd |  5 +++--
 2 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 3dbe0caf..14d4ba82 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -95,7 +95,9 @@ reference:
       - LdEigen-class
       - LdScore-class
       - LdStatistic-class
+      - MashPrior-class
       - MultiStudyQtlDataset-class
+      - SldscData-class
       - SumStatsBase-class
 
   - title: "Class constructors"
@@ -111,10 +113,12 @@ reference:
       - GwasFineMappingResult
       - GwasSumStats
       - LdData
+      - MashPrior
       - MultiStudyQtlDataset
       - QtlDataset
       - QtlFineMappingResult
       - QtlSumStats
+      - SldscData
       - TwasWeights
       - TwasWeightsEntry
 
@@ -226,6 +230,7 @@ reference:
 
   - subtitle: "QtlDataset"
     contents:
+      - getAf
       - getGenotypeCovariates
       - getGenotypes
       - getPhenotypeCovariates
@@ -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
@@ -260,7 +279,7 @@ reference:
   - subtitle: "TwasWeightsEntry"
     contents:
       # Same generic surface as TwasWeights — dispatches on per-row entries.
-      - getCvPerformance
+      - getCvResult
       - getDataType
       - getFits
       - getStandardized
@@ -313,6 +332,7 @@ reference:
       - autoDecision
       - raiss
       - mergeVariantInfo
+      - mergeSusieCs
       - parseCsCorr
       - filterRelatedness
 
@@ -370,6 +390,7 @@ reference:
       - susieAshRssWeights
       - mvsusieWeights
       - mvsusieRssWeights
+      - fsusieWeights
       - fitMvsusie
       - fitMvsusieRss
       - fitFsusie
@@ -470,6 +491,8 @@ reference:
       - computeSldscMRef
       - readAnnotations
       - readSldscTrait
+      - readSldscAnnot
+      - readSldscFrq
       - standardizeSldscTrait
       - h2EstimateToSldscTrait
       - isBinarySldscAnnot
@@ -511,6 +534,7 @@ reference:
       - enlocPipeline
       - ctwasBimfileLoader
       - getCtwasMetaData
+      - mergeCtwasBoundaryRegions
       - loadRegionalAssociationData
       - loadRegionalUnivariateData
       - loadRegionalRegressionData
diff --git a/vignettes/twas-weights.Rmd b/vignettes/twas-weights.Rmd
index 73b39a33..a51c4d95 100644
--- a/vignettes/twas-weights.Rmd
+++ b/vignettes/twas-weights.Rmd
@@ -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
@@ -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.