## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(TENxPBMCData)) require(scry) ## ----------------------------------------------------------------------------- sce<-TENxPBMCData(dataset="pbmc3k") h5counts<-counts(sce) seed(h5counts) #print information about object h5counts<-h5counts[rowSums(h5counts)>0,] system.time(h5devs<-devianceFeatureSelection(h5counts)) # 26 sec ## ----------------------------------------------------------------------------- denseCounts<-as.matrix(h5counts) system.time(denseDevs<-devianceFeatureSelection(denseCounts)) # 5 sec max(abs(denseDevs-h5devs)) #should be close to zero ## ----------------------------------------------------------------------------- mean(denseCounts>0) #shows that the data are mostly zeros so sparsity useful sparseCounts<-Matrix::Matrix(denseCounts,sparse=TRUE) system.time(sparseDevs<-devianceFeatureSelection(sparseCounts)) #1.6 sec max(abs(sparseDevs-h5devs)) #should be close to zero ## ----eval=FALSE--------------------------------------------------------------- # sce <- nullResiduals(sce, assay="counts", type="deviance") # str(sce)