[R] minor allele frequency comparison

[David Winsemius]

On Dec 9, 2011, at 2:44 AM, Scott Harding wrote:

> Hi all,
>
>    We are using two methods to identify SNPs. One is based on  
> resequencing
> the genome and aligning the reads to the sequenced genome to  
> identify SNPs
> (data available for 44 individuals). Another is based on  SNP array  
> with
> selected loci (30000 loci, 870 individuals). I want to compare the  
> results
> from the resequencing based minor allele frequency and Array based  
> minor
> allele frequency. What statistical test should I use?
>
> My table looks like
>
> Chromosome           position               Major/minor
> Resequencing                 SNP array
>
> chromosome 1         198432                 C/T
> 75/13                             1460/280
> chromosome 1         14282752             A/G
> 69/19                             1380/360
> chromosome 1          595434                T/G
> 83/5                               1680/60
>
>
> I really appreciate any guidance.

You will get a much more knowledgeable audience about such questions  
(or at least the currently accepted strategies in your domain) when  
you post this on the Bioconductor mailing list.

>
> Thanks
> Scott
>
> 	[[alternative HTML version deleted]]

I suspect they are also maintaining an HTML-free zone, but I don't  
know for sure. R-help at any rate is an HTML-free mailing list, but  
this post would get encapsulated in the archives in a strange little  
wrapper that requires extra clicking to navigate:

https://stat.ethz.ch/pipermail/r-help/2011-December/298087.html

-- 

David Winsemius, MD
West Hartford, CT