## ----knitr-options, echo=FALSE, message=FALSE, warning=FALSE--------------- ## To render an HTML version that works nicely with github and web pages, do: ## rmarkdown::render("vignettes/vignette.Rmd", "all") library(knitr) opts_chunk$set(fig.align = 'center', fig.width = 6, fig.height = 5, dev = 'png', warning=FALSE, error=FALSE, message=FALSE) library(ggplot2) theme_set(theme_bw(12)) ## ----quickstart-load-data, message=FALSE, warning=FALSE-------------------- library(scater) data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info ) example_sce ## ----quickstart-add-exprs, results='hide'---------------------------------- str(counts(example_sce)) ## -------------------------------------------------------------------------- example_sce$whee <- sample(LETTERS, ncol(example_sce), replace=TRUE) colData(example_sce) rowData(example_sce)$stuff <- runif(nrow(example_sce)) rowData(example_sce) ## ----filter-no-exprs------------------------------------------------------- keep_feature <- rowSums(counts(example_sce) > 0) > 0 example_sce <- example_sce[keep_feature,] ## -------------------------------------------------------------------------- cpm(example_sce) <- calculateCPM(example_sce) ## -------------------------------------------------------------------------- example_sce <- normalize(example_sce) assayNames(example_sce) ## -------------------------------------------------------------------------- identical(exprs(example_sce), logcounts(example_sce)) ## -------------------------------------------------------------------------- assay(example_sce, "is_expr") <- counts(example_sce)>0 ## -------------------------------------------------------------------------- head(calcAverage(example_sce)) ## -------------------------------------------------------------------------- sessionInfo()