[BioC] [Bioc-devel] SNPscan -> SNPchip

[Justin Borevitz]

Hi Rob/Ingo just checking out your SNPchip package and clearly getting Copy
Number Variation (CNV)and SNP calls together from genomic DNA hyb data is
crucial going forward. We and others have developed SNP/tiling arrays for
Arabidopsis and yeast and will hyb genomic DNA to genotype known SNPs/CNVs
AND identify new SFPs and CNVs. Will your package development plans include
dual typing and identification methods? and will you be able to handle SNP
arrays, tiling arrays, and dual SNP/tiling arrays.  Just thought I'd pass
along the direction I see the technology going.
Justin Borevitz

Date: Fri, 3 Nov 2006 07:58:00 -0500
From: Rob Scharpf <rscharpf at jhsph.edu>
Subject:[Bioc-devel] SNPscan -> SNPchip
To: bioc-devel at stat.math.ethz.ch
Message-ID: <EE052468-825B-4B88-978B-1E7A97414761 at jhsph.edu>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Hi,

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/ 
SNP_Annotation_Package_Discussion

Thank you-

Rob and Ingo

rscharpf at jhsph.edu
iruczins at jhsph.edu



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End of Bioc-devel Digest, Vol 32, Issue 4