On 01/31/2013 01:48 PM, Fabrice Tourre wrote: > Valerie, > > Thank you for your reply. > > Is there a function in VariantAnnotation to know whether a snp is > within transcription region but outside coding region? Or is it in > first exon/intron? Yes, the function is called locateVariants(). Use AllVariants() as the 'region' argument and subset your result on the utr and intron regions. From the example below, myregions <- c("intron", "threeUTR", "fiveUTR") loc_coding[loc_coding$LOCATION %in% myregions] Valerie > > On Thu, Jan 31, 2013 at 4:30 PM, Valerie Obenchain <vobencha at="" fhcrc.org=""> wrote: >> Hi Fabrice, >> >> To identify snps (or any ranges) in introns only, use IntronVariants() as >> the 'region' argument. The CodingVariants are the exon regions. If you want >> all regions except coding, I would suggest using AllVariants(). >> >> This output is from the man page example. The 'loc_coding' name is >> misleading since AllVariants were use as 'region'. I have changed it to >> 'loc_all' in the devel branch. >> >>> loc_coding <- locateVariants(vcf_adj, txdb, AllVariants()) >>> loc_coding >> GRanges with 16 ranges and 7 metadata columns: >> seqnames ranges strand | LOCATION QUERYID >> <rle> <iranges> <rle> | <factor> <integer> >> chr1 [ 13220, 13220] * | intron 1 >> chr1 [ 13220, 13220] * | spliceSite 1 >> chr1 [ 13220, 13220] * | intron 1 >> chr1 [ 13220, 13220] * | intron 1 >> chr1 [ 13220, 13220] * | spliceSite 1 >> ... >> ... >> >> This example has variants in splice sites, introns, coding and intergenic >> regions. >> >>> tbl <- table(loc_coding$LOCATION) >>> tbl[tbl > 0] >> >> spliceSite intron coding intergenic >> 2 7 2 5 >> >> The result can be subset on LOCATION for the region of interest. The QUERYID >> column maps back to the row number in the original 'query' argument to >> locateVariants(). >> >> introns <- loc_coding[loc_coding$LOCATION == "intron", ] >>> head(introns, 3) >> GRanges with 3 ranges and 7 metadata columns: >> seqnames ranges strand | LOCATION QUERYID TXID >> <rle> <iranges> <rle> | <factor> <integer> <integer> >> chr1 [13220, 13220] * | intron 1 1 >> chr1 [13220, 13220] * | intron 1 2 >> chr1 [13220, 13220] * | intron 1 3 >> >> >> Valerie >> >> >> >> On 01/31/2013 12:34 PM, Fabrice Tourre wrote: >>> >>> Dear list, >>> >>> I am using VariantAnnotation to Locate variants in and around genes. >>> >>> In VariantAnnotation, the region is defined as: Coding Variants, >>> IntronVariants, FiveUTRVariants, ThreeUTRVariants, IntergenicVariants, >>> SpliceSiteVariants or PromoterVariants. >>> >>> If it possible to know whether a snp is in exon/intron within >>> transcription region but outside coding region? >>> >>> Thanks. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>