## ----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') library(ggplot2) theme_set(theme_bw(12)) ## ----quickstart-load-data, message=FALSE, warning=FALSE-------------------- suppressPackageStartupMessages(library(scater)) data("sc_example_counts") data("sc_example_cell_info") ## ----quickstart-make-sce, results='hide'----------------------------------- example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info) ## ----quickstart-add-exprs, results='hide'---------------------------------- exprs(example_sce) <- log2( calculateCPM(example_sce, use.size.factors = FALSE) + 1) ## ----filter-no-exprs------------------------------------------------------- keep_feature <- rowSums(exprs(example_sce) > 0) > 0 example_sce <- example_sce[keep_feature,] ## ----quick-start-calc-qc-metrics, eval=TRUE-------------------------------- example_sce <- calculateQCMetrics(example_sce, feature_controls = list(eg = 1:40)) ## ----quick-start-gui, eval=FALSE------------------------------------------- # scater_gui(example_sce)