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4.1.4 #30

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4.1.4 #30

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bb9f831
added future max size for v4.1.4
Jun 26, 2025
91727f9
qc resolutions set to 0.01
Riley-Grindle Sep 23, 2025
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4 changes: 4 additions & 0 deletions bin/DoubletFinder.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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6 changes: 5 additions & 1 deletion bin/Merge.R
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Expand Up @@ -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)
Expand Down Expand Up @@ -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)
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8 changes: 4 additions & 4 deletions bin/Normalize_QC.R
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Expand Up @@ -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)
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