[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
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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
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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/
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4. http://news.gmane.org/gmane.science.biology.informatics.conductor
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