Question: karyotype annotation
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gravatar for Nandini B
8.3 years ago by
Nandini B30
Nandini B30 wrote:
Hello, Thank you for your input. But with quanthsmooth, i can generate a karyotype using grid.chromosome which is perfect but I need to annotate specific positions with specific gene names and IDs. is there any way to do this ? Thank you, Warm Regards, Nandini Badarinarayan > From: J.Oosting@lumc.nl > To: nandini_bn@hotmail.com; bioconductor@r-project.org > Subject: RE: [BioC] karyotype annotation > Date: Thu, 21 Apr 2011 07:24:42 +0000 > > The quantsmooth package has a position2cytoband() function you could use > > Jan > > > -----Original Message----- > > From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r- > > project.org] On Behalf Of Nandini B > > Sent: dinsdag 19 april 2011 15:18 > > To: bioconductor@r-project.org > > Subject: [BioC] karyotype annotation > > > > > > Hello, > > > > I have a clustered data which I need to annotate on a karyotype. For > > obtaining the clustering, I have used the heatmap package but are there > > any packages for annotating data on karyotype ? > > > > Thank you, > > > > > > > > > > [[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]]
ADD COMMENTlink modified 8.3 years ago by Oosting, J. PATH550 • written 8.3 years ago by Nandini B30
Answer: karyotype annotation
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gravatar for Oosting, J. PATH
8.3 years ago by
Oosting, J. PATH550 wrote:
You mean something like this: library(quantsmooth) chrom=16 plot(1,xlim=c(0,lengthChromosome(chrom,"bases")), ylim=c(0,4),type="n",xaxt="n",yaxt="n", xlab="",ylab="",main="chromosome 16") paintCytobands(chrom, pos = c(0, 3.5), units = "bases", width = 0.4) text(c(20944476,83841592),c(2,2),c("DNAH3","HSBP1"),srt=90,cex=1.5) Jan > > Hello, > Thank you for your input. But with quanthsmooth, i can generate a > karyotype using grid.chromosome which is perfect but I need to annotate > specific positions with specific gene names and IDs. is there any way to > do this ? > > Thank you, > Warm Regards, > > Nandini Badarinarayan > > > > > > The quantsmooth package has a position2cytoband() function you could use > > > > Jan > > > > > > > > > > > Hello, > > > > > > I have a clustered data which I need to annotate on a karyotype. For > > > obtaining the clustering, I have used the heatmap package but are > there > > > any packages for annotating data on karyotype ? > > > > > > Thank you,
ADD COMMENTlink written 8.3 years ago by Oosting, J. PATH550
hello, Yes, this is what I was looking for. Thank you very much. I appreciate your help! Nandini > From: J.Oosting@lumc.nl > To: nandini_bn@hotmail.com; bioconductor@r-project.org > Subject: RE: [BioC] karyotype annotation > Date: Thu, 21 Apr 2011 11:47:43 +0000 > > You mean something like this: > > library(quantsmooth) > chrom=16 > plot(1,xlim=c(0,lengthChromosome(chrom,"bases")), > ylim=c(0,4),type="n",xaxt="n",yaxt="n", > xlab="",ylab="",main="chromosome 16") > paintCytobands(chrom, pos = c(0, 3.5), units = "bases", width = 0.4) > text(c(20944476,83841592),c(2,2),c("DNAH3","HSBP1"),srt=90,cex=1.5) > > > Jan > > > > > Hello, > > Thank you for your input. But with quanthsmooth, i can generate a > > karyotype using grid.chromosome which is perfect but I need to annotate > > specific positions with specific gene names and IDs. is there any way to > > do this ? > > > > Thank you, > > Warm Regards, > > > > Nandini Badarinarayan > > > > > > > > > > The quantsmooth package has a position2cytoband() function you could use > > > > > > Jan > > > > > > > > > > > > > > > Hello, > > > > > > > > I have a clustered data which I need to annotate on a karyotype. For > > > > obtaining the clustering, I have used the heatmap package but are > > there > > > > any packages for annotating data on karyotype ? > > > > > > > > Thank you, [[alternative HTML version deleted]]
ADD REPLYlink written 8.3 years ago by Nandini B30
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