[BioC] Plotting expression statistic by chromosomal position

Adaikalavan Ramasamy gisar at nus.edu.sg
Thu Aug 14 12:43:48 MEST 2003

Dear all,

I have data of the following format

Genbank Acc ID   Chromosome    Start   Stop   Statistic  
NM_003146                11   313333 316345       3.4 
AK023401                 11   303313 310315      -3.1 
AF086195                 10   613323 716385      -2.2 
NM_314521                21   411233 412341       4.5 

where Start and Stop indicate the start and stop position in the
Chromosome mentioned. Statistics could be fold change or t-statistics. 

I would like to plot the following:
Rows representing Chrosomes 1,2,3, ... , 22, X, Y 
For each gene I would like to color the region from Start to Stop to the
corresponding 'Statistic'

1. There exists a function called amplicon.plot in the geneplotter
library but there is insufficient usage information. Can anyone help me
using this function ?

2. I think amplicon.plot is only capable of showing high and low
expression only (ie. red and blue). Would it be possible to have a range
of colors like a heatmap ?

3. Is there a way for me to get the Chromose, Start and Stop positions
if I give a Genbank Accession ID directly in R ?

Many thanks.

Regards, Adai.

Adaikalavan Ramasamy			gisar at nus.edu.sg
Research Assistant
Microarray & Expression Genomics	Tel: 65-6827 5247
Information & Mathematical Sciences	Fax: 65 6827 5204
Genome Institute of Singapore		www.genomeinstitute.org

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