## ----echo=FALSE, message=FALSE------------------------------------------------ knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) library(BiocStyle) ## ----------------------------------------------------------------------------- library(scRNAseq) sce <- BachMammaryData(samples="G_2") set.seed(1000) sce <- sce[,sample(ncol(sce), 500)] ## ----------------------------------------------------------------------------- library(scuttle) sce <- logNormCounts(sce) library(scran) dec <- modelGeneVar(sce) library(scater) set.seed(1000) sce <- runPCA(sce, ncomponents=10, subset_row=getTopHVGs(dec, n=1000)) library(bluster) clusters <- clusterRows(reducedDim(sce, "PCA"), NNGraphParam()) sce <- runTSNE(sce, dimred="PCA") plotTSNE(sce, colour_by=I(clusters), text_by=I(clusters)) ## ----------------------------------------------------------------------------- library(scDblFinder) tab <- findDoubletClusters(sce, clusters) tab ## ----echo=FALSE--------------------------------------------------------------- # Sanity check that one of the clusters is a good doublet candidate. # If this fails, we probably need to pick a more demonstrative example. stopifnot(rownames(tab)[1]=="6") stopifnot(tab[1,"num.de"]==0) ## ----------------------------------------------------------------------------- sessionInfo()