Question: How to map a SNP to all genes within 50kb (upstream or downstream) of the SNP?
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gravatar for arbet003
2.0 years ago by
arbet00310
arbet00310 wrote:

Hello,

Are there any bioconductor R packages or functions that would allow me to map a SNP to all genes within 50kb (upstream or downstream) of the SNP?

Thanks

snp annotation R • 317 views
ADD COMMENTlink modified 2.0 years ago by James W. MacDonald50k • written 2.0 years ago by arbet00310
Answer: How to map a SNP to all genes within 50kb (upstream or downstream) of the SNP?
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gravatar for James W. MacDonald
2.0 years ago by
United States
James W. MacDonald50k wrote:

Yes. You could use the relevant TxDb package to get the gene locations (say in a GRangesList or GRanges), create a GRanges that defines a 100 kb range centered on your SNP and then use e.g., subsetByOverlaps to subset the genes to just those that are overlapped by your 100kb range. The relevant packages are GenomicAlignments and GenomicFeatures, both of which have vignettes you could read.

ADD COMMENTlink written 2.0 years ago by James W. MacDonald50k
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