[BioC] Help reg Genome view

[James W. MacDonald]

Hi,

First off, please don't take conversations off-list. The archives are 
intended to be a resource for people to search, and if the conversation 
becomes private that function ceases to exist.

On 7/7/2010 3:15 AM, mahalakshmi sivamani wrote:
> Hi,
>
> I visualized the chromosome and genes of the hgu133a array with
> geneplotter package using the following commands,
>
> *library(annotate)
> library(geneplotter)
> library(hgu133a)
> newChrom <- buildChromLocation("hgu133a")
> cPlot(newChrom)

Well you obviously have read the vignette, but evidently didn't 
understand that there is just one step remaining. So here is an example:

library(geneplotter)
library(hgu133a.db)

## note that if you still have a package called hgu133a, then you 
seriously need to update your R and BioC to the release versions.

newChrom <- buildChromLocation("hgu133a")
cPlot(newChrom, c(1:22, "X","Y"))

## Unless you like the extra clutter, I prefer to subset to non-random 
chromosomes

## now fake up some genes - you of course would use the 100 that you are 
interested in

gns <- sample(Lkeys(hgu133aSYMBOL), 100)
cColor(gns, "red", newChrom)

And that, I believe is what you wanted.

Best,

Jim



>
> *I have a list of 100 genes of hgu133a microarray type and its physical
> position. I want to visualize and differentiate those genes from other
> genes of the chromosome.
>
> For Eg,
>
> image.bmp
>
> I have to visualize my genes like the above picture. How can I proceed
> hereafter. Could you please give a good suggestion.
>
> Thanks in advance,
>
> Regards,
>
> S.Mahalakshmi
>
>
> On Tue, Jul 6, 2010 at 6:46 PM, James W. MacDonald
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>> wrote:
>
>     Hi S.Mahalakshmi,
>
>
>     On 7/6/2010 1:11 AM, mahalakshmi sivamani wrote:
>
>         Hi,
>
>         I have a set of genes and its chromosomal physical position in a
>         text file.
>         I want to view those genes in the chromosome using R package
>         GenePlotter.
>         Could any one please tell how to view this.
>
>
>     Have you looked at the vignettes for this package? What have you
>     tried so far?
>
>     You will get much more traction if you show that you have at least
>     made an attempt to figure things out for yourself, and show where
>     things went wrong.
>
>     Best,
>
>     Jim
>
>
>
>         Thanks in advance.
>
>
>         Yours sincerely,
>
>         S.Mahalakshmi
>
>                 [[alternative HTML version deleted]]
>
>         _______________________________________________
>         Bioconductor mailing list
>         Bioconductor at stat.math.ethz.ch
>         <mailto:Bioconductor at stat.math.ethz.ch>
>         https://stat.ethz.ch/mailman/listinfo/bioconductor
>         Search the archives:
>         http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>     --
>     James W. MacDonald, M.S.
>     Biostatistician
>     Douglas Lab
>     University of Michigan
>     Department of Human Genetics
>     5912 Buhl
>     1241 E. Catherine St.
>     Ann Arbor MI 48109-5618
>     734-615-7826
>     **********************************************************
>     Electronic Mail is not secure, may not be read every day, and should
>     not be used for urgent or sensitive issues
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues