[Bioc-devel] SNPscan -> SNPchip

Rob Scharpf rscharpf at jhsph.edu
Fri Nov 3 13:58:00 CET 2006


We changed the name of the R package SNPscan to SNPchip to avoid  
confusion with the SNPscan web-tool.

SNPchip contains classes and methods for organizing and visualizing  
high throughput SNP data.  The classes are indirect extensions of  
eSet.  In particular, we define classes for copy number estimates and  
confidence scores, genotype calls and confidence scores, and a third  
class that contains both copy number and genotype calls.  This third  
class inherits methods from the other two.   We hope that SNPchip  
will provide a useful forum for continued discussion and development  
of these classes.  We will continue to work with Seth and Martin on  
the pros and cons of this setup, hopefully with feedback from other  
bioc-developers.  This feedback may also be useful for improving the  
classes defined in Biobase for SNP data.

As of right now, we provide static tables for SNP- and chromosome- 
level annotation as .RData files.  Annotation packages for Affymetrix  
SNP chips need more discussion.  The wiki for the SNP annotation  
packages is still here: http://wiki.fhcrc.org/bioc/ 

Thank you-

Rob and Ingo

rscharpf at jhsph.edu
iruczins at jhsph.edu

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