[BioC] Plotting expression statistic by chromosomal position
gisar at nus.edu.sg
Thu Aug 14 12:43:48 MEST 2003
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
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 ?
Adaikalavan Ramasamy gisar at nus.edu.sg
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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