Thank you Michael On Tue, Aug 21, 2012 at 9:41 PM, Michael Lawrence <lawrence.michael@gene.com> wrote: > distanceToNearest is going to return a distance, which is always going to > be absolute. If you want to make things positive and negative, then you > will need to call precede and follow and perform a similar calculation. As > long as you have the TSSs in a GRanges, this should work fine. There is no > need for a TranscriptDb. > > Michael > > On Tue, Aug 21, 2012 at 8:29 AM, d r <dolevrahat@gmail.com> wrote: > >> Hello >> >> I want to calculate the distance between HumanMethylation450k probes >> and their nearest TSS using refseq hg19 genes, in such a way that if >> the probe is downstream from the TSS the distance will be assigned a >> positive value, and if the probe is upstream from the TSS, the >> distance will be assigned a negative value. The idea is that both >> strands will be considered. >> >> The distance is to be positive if the nearest TSS is either on the '+ >> strand and its coordinate is greater than the probe's, or of the >> nearest TSS is on the '-' strand and its coordinate is smaller than >> the probe's. >> >> likewise, the distance is to be negative if the nearest TSS is on the >> '+' strand and its coordinate is smaller than the probe's or on the >> '-' strand and its coordinate is grater then the probe's. >> >> It may be possible to do this with transcripts(), but unfortunately my >> dat is not on TranscriptDb >> <http: 127.0.0.1:37980="" help="" library="" genomicfeatures="" help="" transcrip="" tdb=""> >> >> objects. >> >> Is there a way to this using the distanceToNearest method of GRanges? >> >> >> >> thanks >> >> Dolev Rahat >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > [[alternative HTML version deleted]]