Question: GRanges object from gene list
0
gravatar for rbronste
20 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!

ADD COMMENTlink modified 20 months ago • written 20 months ago by rbronste60
Answer: GRanges object from gene list
1
gravatar for Michael Lawrence
20 months ago by
United States
Michael Lawrence11k 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.

ADD COMMENTlink written 20 months ago by Michael Lawrence11k

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()?

ADD REPLYlink written 20 months ago by rbronste60
1

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

ADD REPLYlink written 20 months ago by Michael Lawrence11k
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