## ----include=FALSE------------------------------------------------------------ library(BiocStyle) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("scDblFinder") # # # or, to get that latest developments: # BiocManager::install("plger/scDblFinder") ## ----warning=FALSE------------------------------------------------------------ set.seed(123) suppressPackageStartupMessages(library(scDblFinder)) # we create a dummy dataset; since it's small we set a higher doublet rate sce <- mockDoubletSCE(dbl.rate=0.1, ngenes=300 ) # we run scDblFinder (providing the unusually high doublet rate) sce <- scDblFinder(sce, dbr=0.1) ## ----------------------------------------------------------------------------- table(truth=sce$type, call=sce$scDblFinder.class) ## ----------------------------------------------------------------------------- sce <- scDblFinder(sce, clusters="cluster") table(truth=sce$type, call=sce$scDblFinder.class) ## ----eval=FALSE--------------------------------------------------------------- # library(BiocParallel) # sce <- scDblFinder(sce, samples="sample_id", BPPARAM=MulticoreParam(3)) # table(sce$scDblFinder.class) ## ----------------------------------------------------------------------------- sessionInfo()