Hi, All, I wonder if I can generate an Granges in GenomicFeature for 5kb upstream from start codons, and intergenic region of Drosophila genome, then I can find overlap between my SNP position and GenomicFeature. Like txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene UTR5 <- fiveUTRsByTranscript(txdb) rngs <- GRanges("chr4", IRanges(c(252054, 252561), width=1)) findOverlaps(rngs, UTR5) but not UTR5, replaced by custom GenomicFeature for 5kb upstream from start codons, and intergenic region of Drosophila genome thanks Zhi Zhang, Ph. D. Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Rd. La Jolla, CA 92037, USA Phone 858-646-3100 ext. 3801 Fax 858-795-5298 [[alternative HTML version deleted]]

Hi, On Tue, Dec 6, 2011 at 4:13 PM, Zhi Zhang <zhizhang at="" sanfordburnham.org=""> wrote: > Hi, All, > I wonder if I can generate an Granges in GenomicFeature for 5kb upstream from start codons, and intergenic region of Drosophila genome, then I can find overlap between my SNP position and GenomicFeature. Like > > > > txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene > UTR5 <- fiveUTRsByTranscript(txdb) > rngs <- GRanges("chr4", IRanges(c(252054, 252561), width=1)) > findOverlaps(rngs, UTR5) > > but not UTR5, replaced by custom ?GenomicFeature for 5kb upstream from start codons, and intergenic region of Drosophila genome Let's assume you don't need this in a GRangesList object -- or if you do, I'll let you figure out how to reconstruct the GRangesList from the resulting GRanges below :-) ## use use.names=TRUE here: R> utr5 <- fiveUTRsByTranscript(txdb, use.names=TRUE) R> up5kb <- resize(unlist(utr5), width=5000, fix='end') You'll need to do a bit more bookkeeping if you need to make sure that the 5kb upstream doesn't run into a gene that's less than 5kb away. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact