Wondering about the most straightforward way to take a list of genes and create a GRanges object, so basically pull the intervals for lets say a list of 500 RefSeq genes? Thanks!
It depends on the source. For RefSeq in particular, you could use GenomicFeatures::makeTxDbFromUCSC() and ask for the "refGene" table (I think that's what it's called). Then, extract the desired features as a GRanges with e.g. genes(). There are probably resources available from AnnotationHub, as well.
That would we good for refSeq for sure, how would you approach it if just using official gene symbols, such as those in DESeq2 results()?
You'll want to use whatever annotations were used to generate the counts.