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$", ignore.case = T) SampleNames <- c() -counter <- 1 +counter <- 1 for( file in SeuratRDSfiles){ ObjName <- gsub("^02_","",gsub("_Doublets.*","", file)) SampleNames <- append(SampleNames,ObjName) @@ -94,6 +94,10 @@ dev.off() # ╔══════════════════════════════╗ # ╠═ Scale Merged Seurat Object ═╣ # ╚══════════════════════════════╝ + +# set future max +options(future.globals.maxSize = 4 * 1024^3) # 4 GiB + message("Scaling Merged Seurat Object") # create a list of all genes all.genes <- rownames(MergedSO) diff --git a/bin/Normalize_QC.R b/bin/Normalize_QC.R index 266fd31..9144244 100755 --- a/bin/Normalize_QC.R +++ b/bin/Normalize_QC.R @@ -188,10 +188,10 @@ dev.off() # ╠═ Subset via Metadata ═╣ # ╚═══════════════════════╝ message("Subsetting Seurat Object via Metadata") -minNCount <- quantile(get(NameSO)$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)