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



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