[BioC] Copy number analysis

Fred Boehm fjboehm at wisc.edu
Sat Mar 17 17:24:12 CET 2012


You might want to consider using the bioconductor package "GWASTools". I 
have found it useful for automated detection of baf (ie, B allele 
Frequency) anomalies (and their graphical presentation) with affy 6.0 
data. It would, I think, still require visual inspection of the detected 
chromosomal anomalies if you want to classify them by copy number 
changes. Fortunately, there is a function that plots both BAF and Log R 
Ratio (LRR) for each SNP along a chromosome.

Their is a very instructive vignette that accompanies GWASTools. It is 
called "GWAS Data Cleaning" and can be found via a link from here:


I believe that the "GWAS Data Cleaning" document describes the baf 
anomaly detection methodology and provides detailed code for conducting 
the analyses, starting on page 40.


You can try aroma.affymetrix. Information specific to SNP 6.0 is located at

-----Original Message-----
From:bioconductor-bounces at r-project.org
[mailto:bioconductor-bounces at r-project.org] On Behalf Of Raj [guest]
Sent: Friday, March 16, 2012 5:36 PM
To:bioconductor at r-project.org;drrajan22 at yahoo.com
Subject: [BioC] Copy number analysis

Dear Bioconductor community,

   I am looking for a package for Copy number analysis using CEL file that I
have obtained from Affy SNP 6.0. I have CHP files from birdseed. Now I want
to analyze my data for Copy number and Loss of heterozygosity (using B
allele frequency) and find regions of CN alterations and LOH with or without
Copy number changes. Can anyone direct me to the correct package available
for this?

  -- output of sessionInfo():

R studio

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