Merge branch 'develop' into fix/aggregate_expression

zm19911213 · Nov 15, 2023 · bd0fc57 · bd0fc57
2 parents 77ee042 + b6217b1
commit bd0fc57
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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/differential_expression.R b/R/differential_expression.R
@@ -164,7 +164,7 @@ FindAllMarkers <- function(
           subset = (myAUC > return.thresh | myAUC < (1 - return.thresh))
         )
       } else if (is.null(x = node) || test.use %in% c('bimod', 't')) {
-        gde <- gde[order(gde$p_val, -gde[, 2]), ]
+        gde <- gde[order(gde$p_val, -abs(gde$pct.1-gde$pct.2)), ]
         gde <- subset(x = gde, subset = p_val < return.thresh)
       }
       if (nrow(x = gde) > 0) {
@@ -612,7 +612,7 @@ FindMarkers.default <- function(
   if (test.use %in% DEmethods_nocorrect()) {
     de.results <- de.results[order(-de.results$power, -de.results[, 1]), ]
   } else {
-    de.results <- de.results[order(de.results$p_val, -abs(de.results[,colnames(fc.results)[1]])), ]
+    de.results <- de.results[order(de.results$p_val, -abs(de.results$pct.1-de.results$pct.2)), ]
     de.results$p_val_adj = p.adjust(
       p = de.results$p_val,
       method = "bonferroni",

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')