Bugfix to ClrNormalizeByGroup when ADT not present

Author: bbimber

singlecell/resources/chunks/ClrNormalizeByGroup.R

@@ -1,13 +1,13 @@
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
+
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
     if (!('ADT' %in% names(seuratObj@assays))) {
         print('ADT assay not present, skipping')
-        next
+    } else {
+        seuratObj <- CellMembrane::ClrNormalizeByGroup(seuratObj, groupingVar = groupingVar, assayName = assayName, targetAssayName = targetAssayName, margin = margin, minCellsPerGroup = minCellsPerGroup, calculatePerFeatureUCell = calculatePerFeatureUCell, featureInclusionList = featureWhitelist, featureExclusionList = featureExclusionList, doAsinhTransform = doAsinhTransform)
     }
 
-    seuratObj <- readRDS(seuratObjects[[datasetId]])
-    seuratObj <- CellMembrane::ClrNormalizeByGroup(seuratObj, groupingVar = groupingVar, assayName = assayName, targetAssayName = targetAssayName, margin = margin, minCellsPerGroup = minCellsPerGroup, calculatePerFeatureUCell = calculatePerFeatureUCell, featureInclusionList = featureWhitelist, featureExclusionList = featureExclusionList, doAsinhTransform = doAsinhTransform)
-
     saveData(seuratObj, datasetId)
 
     # Cleanup