The following lines of code has been provided in the pipeline for RNASeqDTU in the following vignette: https://bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html#getting-help

# we can only color because we simulated... col <- rep(8, nrow(dres)) col[rownames(dres) %in% dge.genes] <- 1 col[rownames(dres) %in% dte.genes] <- 2 col[rownames(dres) %in% dtu.genes] <- 3

It has not been shown in the pipeline how to get the dge.genes, dte.genes and dtu.genes part (OR am I missing the part?). I can probably use the 1) gene-ids from the DESeq2 results (after applying logfc and padj cut-offs) for dge.genes and 2) gene-ids from the stageR part for dtu.genes.

Please help. Regards.

These objects are documented in the rnaseqDTU package, see here:

https://github.com/mikelove/rnaseqDTU/tree/master/man

So you can find out more about them with ?dge.genes and they are available with library(rnaseqDTU).