Package/Function to calculate CpG density
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
Hi, Is there a package that has a function to calculate the CpG density between specific locations on a chromosome? thanks! [[alternative HTML version deleted]]
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Neel Aluru ▴ 460
@neel-aluru-3760
Last seen 5.7 years ago
United States
Hey Tim, I just noticed it this week. Follow the link to Rafael Irizarry web site (http://rafalab.jhsph.edu/). They have published a paper on defining CpG islands using R package. Click on "New CpG islands" link in the research overview page. Neel On Nov 6, 2009, at 4:35 PM, Tim Smith wrote: > Hi, > > Is there a package that has a function to calculate the CpG density > between specific locations on a chromosome? > thanks! > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607
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Hi Tim. There are probably more elegant ways, but you might also have a look at the CGcount() function in the MEDME package. It requires a MEDMEset object, but you can create a dummy object with your regions of interest. ?"MEDMEset-class" ?CGcount Quick example: library("MEDME") library("BSgenome.Hsapiens.UCSC.hg18") mms <- new("MEDMEset", chr = rep("chr1",2), pos=c(91642000,91642750), logR=matrix(,nr=2,nc=2,dimnames=list(c("roi1","roi2"))), organism="hsa") CGcount(mms, wsize=250, wFunction="none")@CGcounts This gives for the 2 positions: > CGcount(mms, wsize=250, wFunction="none")@CGcounts chr1 [1] 2 33 ... and if you look in the genome browser, the second region is right in a CpG island, hence the higher score. Cheers, Mark On 7-Nov-09, at 8:40 AM, Neel Aluru wrote: > Hey Tim, > > I just noticed it this week. Follow the link to Rafael Irizarry web > site (http://rafalab.jhsph.edu/). They have published a paper on > defining CpG islands using R package. Click on "New CpG islands" > link in the research overview page. > > Neel > > On Nov 6, 2009, at 4:35 PM, Tim Smith wrote: > >> Hi, >> >> Is there a package that has a function to calculate the CpG density >> between specific locations on a chromosome? >> thanks! >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Neel Aluru > Postdoctoral Scholar > Biology Department > Woods Hole Oceanographic Institution > Woods Hole, MA 02543 > USA > 508-289-3607 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852
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