## ----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----------------------------------------------------------------- names(colData(se)) = "group" dge = DGEList(se) dge ## ----rse------------------------------------------------------------------- dds = as.DESeqDataSet(dge) rse = as(dds, "RangedSummarizedExperiment") rse ## ----sessionInfo----------------------------------------------------------- sessionInfo()