## ----style, echo=FALSE, results='asis'------------------------------------- BiocStyle::markdown() ## ---- message=FALSE-------------------------------------------------------- library(scRNAseq) data(fluidigm) fluidigm ## -------------------------------------------------------------------------- head(assay(fluidigm)[,1:3]) ## -------------------------------------------------------------------------- head(assay(fluidigm, 2)[,1:3]) ## -------------------------------------------------------------------------- names(assays(fluidigm)) head(assays(fluidigm)$fpkm[,1:3]) ## -------------------------------------------------------------------------- dim(fluidigm) table(rowSums(assay(fluidigm))>0) ## -------------------------------------------------------------------------- colData(fluidigm) ## -------------------------------------------------------------------------- names(metadata(fluidigm)) metadata(fluidigm)$which_qc ## -------------------------------------------------------------------------- data(th2) ercc_idx <- grep("^ERCC-", rownames(th2)) th2_endogenous <- th2[-ercc_idx,] th2_ercc <- th2[ercc_idx,] head(assay(th2_ercc)[,1:4])