From 689679779fd84d9916d6500f349af01cb3d2e8a0 Mon Sep 17 00:00:00 2001
From: Eisa Mahyari <eisamahyari@gmail.com>
Date: Sat, 25 May 2019 16:35:03 -0700
Subject: [PATCH] debug seuratfxs

debug normalization integrated
---
 seurat/seuratFunctions.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/seurat/seuratFunctions.R b/seurat/seuratFunctions.R
index 2aa3c5a..98d5e23 100644
--- a/seurat/seuratFunctions.R
+++ b/seurat/seuratFunctions.R
@@ -187,7 +187,8 @@ processSeurat1 <- function(seuratObj, saveFile = NULL, doCellCycle = T, doCellFi
     seuratObj <- markStepRun(seuratObj, 'FilterCells')
   }
   
-  if (forceReCalc | !hasStepRun(seuratObj, 'NormalizeData')) {
+  #other assays like integrated etc do not need normalization
+ if ((forceReCalc | !hasStepRun(seuratObj, 'NormalizeData')) & DefaultAssay(seuratObj)=="RNA") {
     seuratObj <- NormalizeData(object = seuratObj, normalization.method = "LogNormalize", verbose = F)
     seuratObj <- markStepRun(seuratObj, 'NormalizeData', saveFile)
   }