## ----options, include=FALSE, echo=FALSE------------------------------------ library(BiocStyle) knitr::opts_chunk$set(warning=FALSE, error=FALSE, message=FALSE) ## ----construct------------------------------------------------------------- library(SingleCellExperiment) counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10) sce <- SingleCellExperiment(assays = list(counts = counts)) sce ## ----coerce---------------------------------------------------------------- se <- SummarizedExperiment(list(counts=counts)) as(se, "SingleCellExperiment") ## ----fluidigm-------------------------------------------------------------- library(scRNAseq) data(allen) allen sce <- as(allen, "SingleCellExperiment") sce ## ----spikes---------------------------------------------------------------- isSpike(sce, "ERCC") <- grepl("^ERCC-", rownames(sce)) sce ## -------------------------------------------------------------------------- table(isSpike(sce, "ERCC")) spikeNames(sce) ## ----spikes2--------------------------------------------------------------- isSpike(sce, "Adam") <- grepl("^Adam[0-9]", rownames(sce)) sce table(isSpike(sce, "Adam")) spikeNames(sce) ## -------------------------------------------------------------------------- table(isSpike(sce)) ## -------------------------------------------------------------------------- temp <- sce isSpike(temp, "Adam") <- NULL spikeNames(temp) temp <- clearSpikes(temp) spikeNames(temp) ## ----sizeFactors----------------------------------------------------------- sizeFactors(sce) <- colSums(assay(sce)) head(sizeFactors(sce)) ## ----sizeFactors2---------------------------------------------------------- sizeFactors(sce, "ERCC") <- colSums(assay(sce)[isSpike(sce, "ERCC"),]) head(sizeFactors(sce, "ERCC")) head(sizeFactors(sce)) # same as before ## ----metadata-------------------------------------------------------------- colData(sce) rowData(sce) ## ----metadata2------------------------------------------------------------- colData(sce, internal=TRUE) rowData(sce, internal=TRUE) ## ----subset---------------------------------------------------------------- library(magrittr) assay(sce) %>% log1p %>% rowVars -> vars names(vars) <- rownames(sce) vars <- sort(vars, decreasing = TRUE) sce_sub <- sce[names(vars[1:100]),] sce_sub ## ----pca------------------------------------------------------------------- library(Rtsne) set.seed(5252) pca_data <- prcomp(t(log1p(assay(sce_sub)))) tsne_data <- Rtsne(pca_data$x[,1:50], pca = FALSE) reducedDims(sce_sub) <- SimpleList(PCA=pca_data$x, TSNE=tsne_data$Y) sce_sub ## -------------------------------------------------------------------------- reducedDims(sce_sub) reducedDimNames(sce_sub) head(reducedDim(sce_sub, "PCA")[,1:2]) head(reducedDim(sce_sub, "TSNE")[,1:2]) ## -------------------------------------------------------------------------- dim(reducedDim(sce_sub, "PCA")) dim(reducedDim(sce_sub[,1:10], "PCA")) ## -------------------------------------------------------------------------- counts(sce) <- assay(sce, "tophat_counts") sce dim(counts(sce)) ## -------------------------------------------------------------------------- sessionInfo()