[BioC] cPlot

Lavinia Gordon lavinia.gordon at mcri.edu.au
Thu Aug 27 09:12:34 CEST 2009


   Dear Martin
   Thank  you  so  much  for  your  email.   I  had  been  sidetracked by
   'makeProbePackage' and was getting nowhere.
   The instructions in the vignette are very easy to follow, worked a treat for
   both of my sets of data.
   Many thanks,
   Lavinia.
   At 11:01 AM 26/08/2009 -0700, Martin Morgan wrote:

     Lavinia Gordon wrote:
     >    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.
     Hi Lavinia -- you can create your own annotation packages following
     instructions in the 'SqlForge' vignette associated with the
     AnnotationDbi package, available here, for instance
     [1]http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html
     If that is not appropriate (e.g., non-model organism) then for this
     particular case (using cPlot) you could try to construct a
     'chromLocation' object from information you've obtained from other
     sources (e.g., NimbleGen) about chromosome location of each probe. There
     are hints on what this should look like on the help page
     ?"chromLocation-class"; you're aiming to be able to call 'new' with
     appropriate arguments. Some other hints about what the data is supposed
     to look like might come from inspecting the object 'z' produced by the
     code in the cPlot example.
     Martin
     >    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
     >    [1]www.mcri.edu.au
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   Lavinia Gordon
   Research Officer
   Bioinformatics
   Murdoch Childrens Research Institute
   Royal Children's Hospital
   Flemington Road Parkville Victoria 3052 Australia
   telephone: +61 3 8341 6221
   [5]www.mcri.edu.au
   This e-mail and any attachments to it (the "Communication") are, unless
   otherwise stated, confidential, may contain copyright material and is for
   the use only of the intended recipient. If you receive the Communication in
   error, please notify the sender immediately by return e-mail, delete the
   Communication and the return e-mail, and do not read, copy, retransmit or
   otherwise deal with it. Any views expressed in the Communication are those
   of  the individual sender only, unless expressly stated to be those of
   Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its
   related entities. MCRI does not accept liability in connection with the
   integrity  of  or  errors  in  the Communication, computer virus, data
   corruption,  interference  or  delay arising from or in respect of the
   Communication.
   Please consider the environment before printing this email

References

   1. http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html
   2. http://www.mcri.edu.au/
   3. https://stat.ethz.ch/mailman/listinfo/bioconductor
   4. http://news.gmane.org/gmane.science.biology.informatics.conductor
   5. http://www.mcri.edu.au/


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