[BioC] karyotype annotation

[J.Oosting at lumc.nl]

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,