Merge pull request satijalab#666 from satijalab/fix/fix_findmarkers

Fix FindMarkers post Integration/Transfer

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 4.2.0.9001
+Version: 4.2.1.9001
 Date: 2022-09-21
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
@@ -95,7 +95,7 @@ Collate:
     'tree.R'
     'utilities.R'
     'zzz.R'
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 Encoding: UTF-8
 Suggests:
     ape,

NEWS.md

@@ -1,4 +1,9 @@
-# Unreleased
+# Unreleased 
+
+## Changes
+- Fix bug in `FindMarkers()` when run post Integration/Transfer ([#6856](https://github.com/satijalab/seurat/issues/6586))
+
+# Seurat 4.2.1 (2022-11-08)
 
 ## Changes
 - Replaced import from `spatstat.core` with `spatstat.explore`

R/differential_expression.R

@@ -989,9 +989,16 @@ FindMarkers.Seurat <- function(
       command = norm.command,
       value = "normalization.method"
     )
-  } else {
+  } else if (length(x = intersect(x = c("FindIntegrationAnchors", "FindTransferAnchors"), y = Command(object = object)))) {
+    command <- intersect(x = c("FindIntegrationAnchors", "FindTransferAnchors"), y = Command(object = object))[1]
+    Command(
+      object = object,
+      command = command,
+      value = "normalization.method"
+      )
+    } else {
     NULL
-  }
+    }
   de.results <- FindMarkers(
     object = data.use,
     slot = slot,

tests/testthat/test_differential_expression.R

@@ -326,6 +326,34 @@ test_that("FindAllMarkers works as expected", {
   expect_equal(rownames(results.pseudo)[1], "HLA-DPB1")
 })
 
+
+# Tests for running FindMarkers post integration/transfer
+ref <- pbmc_small
+ref <- FindVariableFeatures(object = ref, verbose = FALSE, nfeatures = 100)
+query <- CreateSeuratObject(
+  counts = GetAssayData(object = pbmc_small[['RNA']], slot = "counts") + rpois(n = ncol(pbmc_small), lambda = 1)
+)
+query2 <- CreateSeuratObject(
+  counts = GetAssayData(object = pbmc_small[['RNA']], slot = "counts")[, 1:40] + rpois(n = ncol(pbmc_small), lambda = 1)
+)
+query.list <- list(query, query2)
+query.list <- lapply(X = query.list, FUN = NormalizeData, verbose = FALSE)
+query.list <- lapply(X = query.list, FUN = FindVariableFeatures, verbose = FALSE, nfeatures = 100)
+query.list <- lapply(X = query.list, FUN = ScaleData, verbose = FALSE)
+query.list <- suppressWarnings(lapply(X = query.list, FUN = RunPCA, verbose = FALSE, npcs = 20))
+
+anchors <- suppressMessages(suppressWarnings(FindIntegrationAnchors(object.list = c(ref, query.list), k.filter = NA, verbose = FALSE)))
+object <- suppressMessages(IntegrateData(anchorset = anchors,  k.weight = 25, verbose = FALSE))
+object <- suppressMessages(ScaleData(object, verbose = FALSE))
+object <- suppressMessages(RunPCA(object, verbose = FALSE))
+object <- suppressMessages(FindNeighbors(object = object, verbose = FALSE))
+object <- suppressMessages(FindClusters(object, verbose = FALSE))
+markers <- FindMarkers(object = object, ident.1="0", ident.2="1")
+test_that("FindMarkers recognizes log normalizatio", {
+  expect_equal(markers[1, "p_val"], 1.598053e-14)
+  expect_equal(markers[1, "avg_log2FC"], -2.614686, tolerance = 1e-6)
+})
+
 # Tests for FindConservedMarkers
 # -------------------------------------------------------------------------------