Entering edit mode
Justin Borevitz
▴
170
@justin-borevitz-1002
Last seen 10.0 years ago
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@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
------------------------------
_______________________________________________
Bioc-devel mailing list
Bioc-devel at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioc-devel
End of Bioc-devel Digest, Vol 32, Issue 4