From bb9f831ef2ae0d466e641da9d65a2bf868ff82f1 Mon Sep 17 00:00:00 2001
From: Ryan <rseaman@mdibl.org>
Date: Thu, 26 Jun 2025 11:30:41 -0400
Subject: [PATCH 1/2] added future max size for v4.1.4

---
 bin/DoubletFinder.R | 4 ++++
 bin/Merge.R         | 6 +++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/bin/DoubletFinder.R b/bin/DoubletFinder.R
index c6ce0e1..fab59e1 100755
--- a/bin/DoubletFinder.R
+++ b/bin/DoubletFinder.R
@@ -54,6 +54,10 @@ params.scaleMethod <- args[6]
 # ╔═════════════════════════════════╗
 # ╠═ Preparation for Find Doublets ═╣
 # ╚═════════════════════════════════╝
+
+# set future max
+options(future.globals.maxSize = 4 * 1024^3)  # 4 GiB
+
 message("Preparing for Find Doublets")
 # read in .rds
 samp <- readRDS(params.SeuratObject)
diff --git a/bin/Merge.R b/bin/Merge.R
index 0502376..a0dae13 100755
--- a/bin/Merge.R
+++ b/bin/Merge.R
@@ -52,7 +52,7 @@ message("Loading in Seurat Objects")
 SeuratRDSfiles <- list.files(pattern = "\\.rds$", ignore.case = T)
 SampleNames <- c()
 
-counter <- 1 
+counter <- 1
 for( file in SeuratRDSfiles){
     ObjName <- gsub("^02_","",gsub("_Doublets.*","", file))
     SampleNames <- append(SampleNames,ObjName)
@@ -94,6 +94,10 @@ dev.off()
 # ╔══════════════════════════════╗
 # ╠═ Scale Merged Seurat Object ═╣
 # ╚══════════════════════════════╝
+
+# set future max
+options(future.globals.maxSize = 4 * 1024^3)  # 4 GiB
+
 message("Scaling Merged Seurat Object")
 # create a list of all genes
 all.genes <- rownames(MergedSO)

From 91727f9460174d47fd89904603f8ed75fdcb5ce4 Mon Sep 17 00:00:00 2001
From: Riley-Grindle <122935497+Riley-Grindle@users.noreply.github.com>
Date: Tue, 23 Sep 2025 14:14:44 -0400
Subject: [PATCH 2/2] qc resolutions set to 0.01

---
 bin/Normalize_QC.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/bin/Normalize_QC.R b/bin/Normalize_QC.R
index 266fd31..9144244 100755
--- a/bin/Normalize_QC.R
+++ b/bin/Normalize_QC.R
@@ -188,10 +188,10 @@ dev.off()
 # ╠═ Subset via Metadata ═╣
 # ╚═══════════════════════╝
 message("Subsetting Seurat Object via Metadata")
-minNCount         <- quantile(get(NameSO)$nCount_RNA, probs = seq(0,1,0.05))[[paste0(params.ncount_lower, "%")]]
-minNFeature       <- quantile(get(NameSO)$nFeature_RNA, probs = seq(0,1,0.05))[[paste0(params.nfeature_lower, "%")]]
-maxNCount         <- quantile(get(NameSO)$nCount_RNA, probs = seq(0,1,0.05))[[paste0(params.ncount_upper, "%")]]
-maxNFeature       <- quantile(get(NameSO)$nFeature_RNA, probs = seq(0,1,0.05))[[paste0(params.nfeature_upper, "%")]]
+minNCount         <- quantile(get(NameSO)$nCount_RNA, probs = seq(0,1,0.01))[[paste0(params.ncount_lower, "%")]]
+minNFeature       <- quantile(get(NameSO)$nFeature_RNA, probs = seq(0,1,0.01))[[paste0(params.nfeature_lower, "%")]]
+maxNCount         <- quantile(get(NameSO)$nCount_RNA, probs = seq(0,1,0.01))[[paste0(params.ncount_upper, "%")]]
+maxNFeature       <- quantile(get(NameSO)$nFeature_RNA, probs = seq(0,1,0.01))[[paste0(params.nfeature_upper, "%")]]
 maxMitoPct        <- as.integer(params.mito_pct)
 
 print(minNFeature)