I have the following object in a basic DESeq2 bulk RNA-seq differential expression pipeline (human data). It filters out the genes that have low counts but on top of that I would like to remove a couple of genes that I know have issues in my dataset, and want to see how my analysis looks without them. I have the list of such genes in a vector named "genes" and it's encoded as gene symbols (I could transform them to EnsemblIDs if needed).
genesToRemove<- c("gene1","gene2","gene3","gene4","gene5","gene6") dds <- DESeqDataSetFromHTSeqCount(sampleTable = mytable,directory = directory,design= ~ condition) dds class: DESeqDataSet dim: 60725 326 metadata(1): version assays(1): counts rownames(60725): ENSG00000278625.1 ... ENSG00000277374.1 rowData names(0): colnames(326): 9275 9351 ... 10146 10199 colData names(5): Condition Age ... genes_to_keep <- rowSums(counts(dds)) >= 50 dds2 <- dds[genes_to_keep,]
I would like to do it at this point, after this code, so that then I keep going without them. The problem is that I am not sure how to access the part of the dds2 object where you have the genes in order to filter them out. Any thoughts? Thank you.