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Single-cell transcriptomics/2_DoubletFinder_2.R

+#### Packages loading
+
+library(Matrix)
+library(Seurat)
+library(dplyr)
+library(ggplot2)
+library(DoubletFinder)
+library(KernSmooth)
+library(ROCR)
+
+for (sample in c("C2-DC2093","C2-DC2158")) {
+Data<-readRDS(paste0("3-DoubletFinder/",sample,"/Data.rds"))
+if (sample=="C2-DC2093"){UsingDim=8} else  {if (sample=="C2-DC2158"){UsingDim=9}}
+
+Data<-FindNeighbors(Data,dims=1:UsingDim)
+Data<-FindClusters(Data,resolution=0.6)
+head(Idents(Data),5)
+
+#### pK Identification (no ground-truth)
+sweep.res.list <- paramSweep_v3(Data, PCs = 1:10, sct = FALSE)
+sweep.stats <- summarizeSweep(sweep.res.list, GT = FALSE)
+bcmvn <- find.pK(sweep.stats)
+
+pdf(file=paste0("3-DoubletFinder/",sample,"/Choose pK.pdf"),width=10,height=9)
+print(ggplot(bcmvn, aes(x=pK, y=BCmetric)) + geom_point() + geom_line(aes(group=1)))
+dev.off()
+
+saveRDS(Data,file=paste0("3-DoubletFinder/",sample,"/Data2.rds"))
+}