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.