[BioC] cPlot

[Lavinia Gordon]

   Dear All,
   Following on from Axels email, this is exactly what I would like to do, but
   I am not using Affymetrix data.  Can anyone give me some pointers on how to
   create  an  Bioconductor  data package (i.e. like hgug41112a), but for
   NimbleGen data.
   with many thanks for your time,
   Lavinia Gordon.

     Message: 6
     Date: Mon, 24 Aug 2009 19:15:29 +0200
     From: Axel.Klenk at Actelion.Com
     Subject: [BioC] chromosome ordering in cPlot()/cColor()
     To: bioconductor at stat.math.ethz.ch
     Message-ID:
             <12450_1251134133_4A92CAB5_12450_361234_1_OFDD2C6357.89EE7981-ONC1
     25761C.005CC5F4-C125761C.005ECE81 at actelion.com>

     Content-Type: text/plain; charset=US-ASCII
     Dear Biocore Team,
     I'm using cPlot()/cColor() from package annotate to produce chromosome
     plots and
     am very impressed how easily this can be achieved. However, unfortunately,
     the
     chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11,
     etc.
     from bottom
     to top and I would like to reorder them to 1, 2, 3, ... from top to bottom
     but cannot find an
     easy way to do so... am I missing something here?
     I managed to get what I want by hacking buildChromLocation() but that's
     ugly and I don't
     want to maintain a modified function if not necessary.
     Would it be possible to add a replace method for the chromInfo slot to
     allow e.g.
     z <- buildChromLocation("hgug41112a")
     library("gtools") # for mixedsort()
     info <- chromInfo(z)
     chromInfo(z) <- info[rev(mixedsort(names(info)))]
     or maybe you can think of a better solution?
     Thanks in advance,
      - axel
     Axel Klenk
     Research Informatician
     Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
     Switzerland

   Lavinia Gordon
   Research Officer
   Bioinformatics
   Murdoch Childrens Research Institute
   Royal Children's Hospital
   Flemington Road Parkville Victoria 3052 Australia
   telephone: +61 3 8341 6221
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