[BioC] Gene Mapping on Chrosmosomes

[Furge, Kyle]

I think the general sequence would be:

1) read in the data files using something like read.delim()
2) make sure you have the hgu95av2 meta data package installed
3) use something like buildChromLocation() from the annotation package to
associate probe ids with genomic location
4) use something like geneplotter, chromViz, or the ideogram package to plot
the data. The specifics of these packages vary, but they mostly take the
same types of data structures

-kyle

##
## Example code: Do not run
##

my_data <- read.delim("my_file")

## lets say there are columns called RAW and ID in the file

raw_data <- my_data[,"RAW"]
names(raw_data) <- my_data[,"ID"]

## do some plots

library(hgu95av2)
cL <- buildlChromLocation("hgu95av2")

library(ideogram)
mideogram(raw_data,cL)



> From: Hrishikesh Deshmukh <d_hrishikesh at yahoo.com>
> Date: Fri, 11 Nov 2005 06:25:26 -0800 (PST)
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Gene Mapping on Chrosmosomes
> 
> Dear All,
> 
> I have 4000 genes (HG_U94Av2, tab separated) files
> with signal intensities, how can i map the position of
> each gene on human chromosomes and if possible plot
> signal intensities, log and raw.
> 
> This is my first stab at this, so kindly pardon my
> ignorance on this issue.
> 
> Thanks,
> Hrishi
> 
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