## ----library, message=FALSE----------------------------------------------
library(DESeq2)
library(edgeR)
library(DEFormats)

## ----counts--------------------------------------------------------------
counts = simulateRnaSeqData()

## ----headcounts----------------------------------------------------------
head(counts)

## ----dge-----------------------------------------------------------------
group = rep(c("A", "B"), each = 3)

dge = DGEList(counts, group = group)
dge

## ----dds-----------------------------------------------------------------
dds = as.DESeqDataSet(dge)
dds

## ----dgedds--------------------------------------------------------------
identical(dge, as.DGEList(dds))

## ----identicalDDS--------------------------------------------------------
dds1 = DESeqDataSetFromMatrix(counts, data.frame(condition=group), ~ condition)
dds2 = DESeqDataSetFromMatrix(counts, data.frame(condition=group), ~ condition)

identical(dds1, dds2)

## ----se------------------------------------------------------------------
se = simulateRnaSeqData(output = "RangedSummarizedExperiment")
se

## ----dds_se--------------------------------------------------------------
dds = DESeqDataSet(se, design = ~ condition)

## ----dgedds2-------------------------------------------------------------
dge = as.DGEList(dds)
dge

## ----dgeSE---------------------------------------------------------------
dge = DGEList(se)
dge

## ----rse-----------------------------------------------------------------
dds = as.DESeqDataSet(dge)
rse = as(dds, "RangedSummarizedExperiment")
rse

## ----sessionInfo---------------------------------------------------------
sessionInfo()