quickCorrect returns all genes by default after correcting on HVGs.

R/quickCorrect.R

@@ -23,6 +23,10 @@
 #' These genes will be used in the correction, though corrected values for all genes can be returned by setting \code{correct.all=TRUE}.
 #' \item Applying the batch correction algorithm of choice with \code{\link{batchCorrect}}, as specified by \code{PARAM}.
 #' }
+#' 
+#' The default of \code{correct.all=TRUE} differs from that of other functions.
+#' This is because the subsetting to HVGs is done internally here, and we avoid surprises by returning results for all genes in the input object(s).
+#' In contrast, the other functions require explicit subsetting via \code{subset.row=} and it is expected that users will set \code{correct.all=} if all genes are desired.
 #'
 #' @return A list containing:
 #' \itemize{
@@ -62,7 +66,7 @@
 quickCorrect <- function(..., 
     batch=NULL, 
     restrict=NULL, 
-    correct.all=FALSE, 
+    correct.all=TRUE, 
     assay.type="counts", 
     PARAM=FastMnnParam(), 
     multi.norm.args=list(),

tests/testthat/test-quick-correct.R

@@ -52,12 +52,14 @@ test_that("quickCorrect works with a single object", {
 })
 
 test_that("quickCorrect actually uses its HVGs", {
-    set.seed(0)
-    pre1 <- quickCorrect(sce1, sce2, hvg.args=list(n=20))
+    BPPARAM <- FastMnnParam(d=10) # avoid warnings
 
     set.seed(0)
-    pre2 <- quickCorrect(sce1, sce2, hvg.args=list(n=100))
+    pre1 <- quickCorrect(sce1, sce2, PARAM=BPPARAM, hvg.args=list(n=50))
+    set.seed(0)
+    pre2 <- quickCorrect(sce1, sce2, PARAM=BPPARAM, hvg.args=list(n=100))
 
     # Actually has an effect.
-    expect_false(identical(pre1, pre2))
-})
+    expect_false(identical(pre1$corrected, pre2$corrected))
+    expect_identical(nrow(pre1$corrected), nrow(pre2$corrected)) # negative control
+q})