## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## pre-load to avoid load messages in report library(Glimma) library(edgeR) library(DESeq2) ## ----------------------------------------------------------------------------- library(Glimma) library(edgeR) library(DESeq2) dge <- readRDS(system.file("RNAseq123/dge.rds", package = "Glimma")) dds <- DESeqDataSetFromMatrix( countData = dge$counts, colData = dge$samples, rowData = dge$genes, design = ~group ) ## ----------------------------------------------------------------------------- glimmaMDS(dds) ## ----------------------------------------------------------------------------- dds <- DESeq(dds, quiet=TRUE) ## ----------------------------------------------------------------------------- glimmaMA(dds) ## ----eval = FALSE------------------------------------------------------------- # # creates ma-plot.html in working directory # # link to it in Rmarkdown using [MA-plot](ma-plot.html) # htmlwidgets::saveWidget(glimmaMA(dds), "ma-plot.html") ## ----------------------------------------------------------------------------- sessionInfo()