## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("SCArray") ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(SCArray)) suppressPackageStartupMessages(library(SingleCellExperiment)) # load a SingleCellExperiment object fn <- system.file("extdata", "LaMannoBrainSub.rds", package="SCArray") sce <- readRDS(fn) # convert to a GDS file scConvGDS(sce, "test.gds") # list data structure in the GDS file (f <- scOpen("test.gds")); scClose(f) ## ----------------------------------------------------------------------------- library(Matrix) cnt <- matrix(0, nrow=4, ncol=8) set.seed(100); cnt[sample.int(length(cnt), 8)] <- rpois(8, 4) (cnt <- as(cnt, "dgCMatrix")) # convert to a GDS file scConvGDS(cnt, "test.gds") ## ----------------------------------------------------------------------------- # a GDS file in the SCArray package (fn <- system.file("extdata", "LaMannoBrainData.gds", package="SCArray")) # load a SingleCellExperiment object from the file sce <- scExperiment(fn) sce # it is a DelayedMatrix (the whole matrix is not loaded) assays(sce)$counts # column data colData(sce) # row data rowData(sce) ## ----------------------------------------------------------------------------- cnt <- assays(sce)$counts logcnt <- log2(cnt + 1) assays(sce)$logcounts <- logcnt logcnt ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(DelayedMatrixStats)) col_mean <- DelayedMatrixStats::colMeans2(logcnt) str(col_mean) row_mean <- DelayedMatrixStats::rowMeans2(logcnt) str(row_mean) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(scater)) # run umap analysis sce <- runUMAP(sce) ## ----fig.width=4,fig.height=3------------------------------------------------- plotReducedDim(sce, dimred="UMAP") ## ----------------------------------------------------------------------------- # print version information about R, the OS and attached or loaded packages sessionInfo() ## ----echo=FALSE--------------------------------------------------------------- unlink("test.gds", force=TRUE)