## ----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()