I currently have an RNA-seq dataset where I've quantified counts by regions that don't line up neatly to existing genes. Currently, I've created a DESeq dataset from my count matrix (not from the raw alignments), and running assay(dds) resembles something like:
Exp1 Exp2 Exp3 Exp4 ID1 2 4 8 5 ID2 9 45 3 12
And so on. It's trivial for me to take each ID name and create a corresponding annotation for it that includes the feature's chromosome, strand, and start/end coordinates. This leaves me with a data.frame in the form:
Chrom Strand Start End ID1 IV + 100 300 ID2 II - 2847 2904
And so on. How do I add this annotation data to my current DESeq dataset object? My aim is to be able to visualize my significant LFC enriched sites using the GViz package as described here. However, first I just need to add these coordinate annotations. How do I do this? I know that it involves constructing a GRanges object somehow and then adding it to the rowRanges of the DESeq dataset, but I'm not yet sure how to construct this from my existing data.frame.