## ----style, echo=FALSE, results='hide', message=FALSE---------------------- library(BiocStyle) library(knitr) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) opts_chunk$set(fig.asp=1) ## -------------------------------------------------------------------------- library(TENxBrainData) sce <- TENxBrainData20k() # downloads once and caches it for future use. sce ## -------------------------------------------------------------------------- counts(sce) object.size(counts(sce)) file.info(path(counts(sce)))$size ## -------------------------------------------------------------------------- tmp <- counts(sce) tmp <- log2(tmp + 1) tmp ## -------------------------------------------------------------------------- library(scater) sce <- calculateQCMetrics(sce, compact=TRUE) # compacting for clean output. sce$scater_qc ## -------------------------------------------------------------------------- bpp <- MulticoreParam(2) bpp ## -------------------------------------------------------------------------- bpp <- SnowParam(5) bpp ## ---- eval=FALSE----------------------------------------------------------- # bpp <- BatchtoolsParam(10, cluster="slurm", # resources=list(walltime=20000, memory=8000, ncpus=1)) ## -------------------------------------------------------------------------- alt <- calculateQCMetrics(sce, BPPARAM=MulticoreParam(2), compact=TRUE) ## ---- echo=FALSE----------------------------------------------------------- if (!isTRUE(all.equal(alt, sce))) { stop("parallelization changes the result") } ## -------------------------------------------------------------------------- all.equal(alt, sce) ## -------------------------------------------------------------------------- sce.pbmc <- readRDS("pbmc_data.rds") ## -------------------------------------------------------------------------- library(scran) library(BiocNeighbors) snn.gr <- buildSNNGraph(sce.pbmc, BNPARAM=AnnoyParam(), use.dimred="PCA") ## -------------------------------------------------------------------------- clusters <- igraph::cluster_walktrap(snn.gr) table(Exact=sce.pbmc$Cluster, Approx=clusters$membership) ## -------------------------------------------------------------------------- sessionInfo()