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Question: GRanges object from gene list
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4 months ago by
rbronste60
rbronste60 wrote:

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!

modified 4 months ago • written 4 months ago by rbronste60
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4 months ago by
Michael Lawrence10.0k
United States
Michael Lawrence10.0k wrote:

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()?

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You'll want to use whatever annotations were used to generate the counts.