Tim, Thank you very much. It is really helpful to me. I learn a lot from your reply. Best wishes, On Fri, Feb 8, 2013 at 12:51 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > Minor derp: > > values(vars)[, c(1,2,3,5,6,7)] ## so that it fits in an email :-) > > ## was actually run as > > values(vars)[, c(1,5,6,7)] > > ## my bad > > > > > On Fri, Feb 8, 2013 at 9:50 AM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> > wrote: >> >> suppose you have your SNPs in a data.frame named 'SNPs' with columns >> 'chrom' and 'location', and suppose they're called against hg19. Say, >> >> SNPs <- data.frame(chrom=c('chr1','chr9'), location=c(123, 456)) >> >> ## To use locateVariants easily, you'll want to turn them into a GRanges. >> >> library(GenomicRanges) >> SNPs.gr <- GRanges( seqnames=SNPs$chrom, >> IRanges(start=SNPs$location, >> width=1) ) >> genomeSNPs.gr) <- 'hg19' ## always record your genome, always always >> >> ## Then: >> >> library(Homo.sapiens) >> library(VariantAnnotation) >> >> vars <- locateVariantsSNPs.gr, ## the following is from Homo.sapiens >> TxDb.Hsapiens.UCSC.hg19.knownGene, >> AllVariants()) >> >> values(vars)[, c(1,2,3,5,6,7)] ## so that it fits in an email :-) >> ## DataFrame with 2 rows and 4 columns >> ## LOCATION GENEID PRECEDEID FOLLOWID >> ## 1 intergenic NA 79501 653635 >> ## 2 intergenic NA 81704 100287171 >> >> ## As the above are both intergenic, you might like to know what they're >> near: >> ## >> unlist(mget(vars$PRECEDEID, org.Hs.egSYMBOL)) ## from Homo.sapiens >> ## 79501 81704 >> ## "OR4F5" "DOCK8" >> >> unlist(mget(vars$FOLLOWID, org.Hs.egSYMBOL)) ## from Homo.sapiens >> ## 653635 100287171 >> ## "WASH7P" "WASH1" >> >> Does this make sense? >> >> It is a tremendously useful package (thanks much to Valerie, Martin, >> Michael and Stephanie). >> >> >> On Fri, Feb 8, 2013 at 9:29 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> >> wrote: >>> >>> Dear list, >>> >>> I am using VariantAnnotation package to annotated a list of snps. But >>> I only have the snp coordinate information. It seems VariantAnnotation >>> only works with VCF format. I am not family with VCF format. >>> >>> How can I use VariantAnnotation with my snp list? It is not vcf format. >>> >>> >>> Thank you very much in advance. >>> >>> Best wishes, >>> >>> _______________________________________________ >>> 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 >> >> >> >> >> -- >> A model is a lie that helps you see the truth. >> >> Howard Skipper > > > > > -- > A model is a lie that helps you see the truth. > > Howard Skipper