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Question: GRanges object from gene list
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gravatar for rbronste
4 weeks ago by
rbronste50
rbronste50 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 4 weeks ago • written 4 weeks ago by rbronste50
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gravatar for Michael Lawrence
4 weeks ago by
United States
Michael Lawrence9.9k 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 4 weeks ago by Michael Lawrence9.9k

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 4 weeks ago by rbronste50
1

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

ADD REPLYlink written 4 weeks ago by Michael Lawrence9.9k
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