Thanks. That's very helpful. Regards, Khadeeja ________________________________ From: "Tim Triche, Jr." <tim.triche@gmail.com> Cc: bioconductor@stat.math.ethz.ch Sent: Wednesday, December 14, 2011 9:51 PM Subject: Re: [BioC] Distance from TSS and CPG I wrote this up as an example in the IlluminaHumanMethylation450kprobe package... which seemingly disappeared into thin air after uploading it! � Oh well. IlluminaHumanMethylation450kprobe for this and several other common use cases, otherwise here's the man page and data.frame... hopefully it makes sense. �(There is a similar object in the .db package but without any sequences) For what you want, you could just do (even with the crufty old 1.4.6 .db package) > library(IlluminaHumanMethylation450k.db) > sites <- toTable(IlluminaHumanMethylation450kCPG37) # or CPG36 if using hg18 > chrs <-�toTable(IlluminaHumanMethylation450kCHR37) # or CHR36 if using hg18 > coords <- merge(sites, chrs, by='Probe_ID') > names(coords) <- c('probe','site','chr') > head(coords) � � � �probe � � �site chr 1 cg00000029 �53468112 �16 2 cg00000108 �37459206 � 3 3 cg00000109 171916037 � 3 4 cg00000165 �91194674 � 1 5 cg00000236 �42263294 � 8 6 cg00000289 �69341139 �14 >�library(GenomicFeatures) > CpGs.unstranded <- with(coords,� � � � � � � � � � � � � � GRanges(paste('chr',chr,sep=''), � � � � � � � � � � � � � � � � � IRanges(start=site, width=1, names=probe))) >�refgene.TxDb = makeTranscriptDbFromUCSC('refGene', genome='hg19') > TSS.forward = transcripts(refgene.TxDb,� � � � � � � � � � � � � � � vals=list(tx_strand='+'),� � � � � � � � � � � � � � � columns='gene_id') > nearest.fwd = precede(CpGs.unstranded, TSS.forward) > nearest.fwd.eg = nearest.fwd # to keep dimensions right > notfound = whichis.na(nearest.fwd)) # track for later� > nearest.fwd.eg[-notfound] =� � � as.character(elementMetadata(TSS.forward)$gene_id[nearest.fwd[-not found]]) > TSSs.fwd = start(TSS.forward[nearest.fwd[-notfound]]) > distToTSS.fwd = nearest.fwd # to keep dimensions right > distToTSS.fwd[-notfound] = start(CpGs.unstranded)[-notfound] - TSSs.fwd And likewise with vals=list(tx_strand='-') for the reverse strand. � For CpG island distance you will need to decide which CpG island definition to use. �Personally I like Irizarry's. �Once you have constructed a GRanges object with the start and end coordinates of the CpG islands, most of it will be equally straightforward.� Hi, > >I have a list of probes from IlluminaHumanMethylation450k array, and I need to >find the distance from TSS and also the distance from CpG island for each. Is >there a simple way to do this? > >Thanks in advance, >Khadeeja > >_______________________________________________ >Bioconductor mailing list >Bioconductor@r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann [[alternative HTML version deleted]]