Merge branch 'develop' into ig_marker_sorting

zm19911213 · Nov 10, 2023 · 2ddf7f4 · 2ddf7f4
2 parents 7cbd77d + 79c2bec
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# Unreleased
+
+## Changes
+
+- Fixed `SCTransform.StdAssay` to pass extra arguments to `sctransform::vst()`. Fixes [#875](https://github.com/satijalab/seurat/issues/7998)
+
+
 # Seurat 5.0.0 (2023-10-25)
 
 ## Added

diff --git a/R/preprocessing5.R b/R/preprocessing5.R
@@ -1260,7 +1260,8 @@ SCTransform.StdAssay <- function(
                             conserve.memory = conserve.memory,
                             return.only.var.genes = return.only.var.genes,
                             seed.use = seed.use,
-                            verbose = verbose)
+                            verbose = verbose,
+                            ...)
     min_var <- vst.out$arguments$min_variance
     residual.type <- vst.out[['residual_type']] %||% 'pearson'
     assay.out <- CreateSCTAssay(vst.out = vst.out, do.correct.umi = do.correct.umi, residual.type = residual.type,

diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -402,7 +402,7 @@ BEGIN_RCPP
 END_RCPP
 }
 
-RcppExport SEXP isnull(void *);
+RcppExport SEXP isnull(SEXP);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_Seurat_RunModularityClusteringCpp", (DL_FUNC) &_Seurat_RunModularityClusteringCpp, 9},

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,10 +1,10 @@
 library(testthat)
 library(Seurat)
-
-# Run tests for 'v3'
-message('Run tests for v3 assay')
-options(Seurat.object.assay.version = 'v3')
-test_check("Seurat")
+#
+# # Run tests for 'v3'
+# message('Run tests for v3 assay')
+# options(Seurat.object.assay.version = 'v3')
+# test_check("Seurat")
 
 # Run tests for 'v5'
 message('Run tests for v5 assay')