[BioC] R functions for genetic distances

[Waddell, Peter J]

Hello,

I hoped you could help. The original querry is:

>> We are now looking for a prior step that can convert our data into
>> population frequencies. The data we have are in SNP frequencies and
>> the
>> format of the data are
>> 
>>    ind1 ind2 ind3 ind4
>> Loc1 AA   AC   CC   AC
>> Loc2 CC   CT   --   CT
>> 
>> And so on. We need to preprocess so that we select which columns
>> from which
>> populations. We also need to interpret the genotypes correctly (and
>> note
>> that -- is missing data).
>> 
>> Do you know of any R routines that can do this? Does APE have this
>> functionality? The data are from the Illumina beadstation SNP caller.

I see that bioconductor can call SNP's from the raw data, but I did not see
a link to the follow up we need prior to estimating genetic distances of
populations.

Thanks,

Peter.


On 5/18/10 2:24 PM, "Brian O'Meara" <omeara.brian at gmail.com> wrote:

> Hi, Peter. I don't know what can do what you want (I'd be tempted to
> write something treating the input data as factors). I don't think APE
> can do this. However, you should look at http://www.bioconductor.org
> -- it has a set of 389 packages for genomic analysis, several of which
> deal with SNP data (there are even packages for processing raw tiff
> data from Illumina beadarrays
> (<http://www.bioconductor.org/packages/release/bioc/html/beadarray.html
>> )). You might also look at the Genetics task view for relevant
> packages (<http://cran.r-project.org/web/views/Genetics.html>)
> 
> Hope this helps,
> Brian
> 
> On May 18, 2010, at 2:09 PM, Waddell, Peter J wrote:
> 
>> Hello,
>> 
>> Could you please help me to contact Daniel and/or help answer the
>> questions
>> below.
>> 
>> Many thanks,
>> 
>> Peter.
>> 
>> 
>> ------ Forwarded Message
>> From: "Waddell, Peter J" <pwaddell at purdue.edu>
>> Date: Mon, 17 May 2010 18:06:11 -0400
>> To: "chessel at biomserv.univ-lyon1.fr" <chessel at biomserv.univ-lyon1.fr>
>> Cc: "khan27 at purdue.edu" <khan27 at purdue.edu>
>> Subject: R functions for genetic distances
>> 
>> Dear Daniel,
>> 
>> We were very pleased to find your R routines to calculate genetic
>> distances
>> in R, in particular, Nei's, Reynold et al. etc. distances.
>> 
>> We are now looking for a prior step that can convert our data into
>> population frequencies. The data we have are in SNP frequencies and
>> the
>> format of the data are
>> 
>>    ind1 ind2 ind3 ind4
>> Loc1 AA   AC   CC   AC
>> Loc2 CC   CT   --   CT
>> 
>> And so on. We need to preprocess so that we select which columns
>> from which
>> populations. We also need to interpret the genotypes correctly (and
>> note
>> that -- is missing data).
>> 
>> Do you know of any R routines that can do this? Does APE have this
>> functionality? The data are from the Illumina beadstation SNP caller.
>> 
>> Many thanks,
>> 
>> Peter Waddell.
>> 
>> 
>> On 5/17/10 5:28 PM, "khan27 at purdue.edu" <khan27 at purdue.edu> wrote:
>> 
>>> 
>>> functions :
>>> genet.html
>>> dist.genet
>>> 
>>> Author:
>>> Daniel Chessel chessel at biomserv.univ-lyon1.fr
>>> 
>>> Link:
>>> http://pbil.univ-lyon1.fr/ade4html/
>>> 
>>> Thanks,
>>> 
>>> Ishita
>> 
>> 
>> ------ End of Forwarded Message
>> 
> 
> ------------------------------------------------------
> Brian O'Meara
> http://www.brianomeara.info
> Assistant Prof.
> Dept. Ecology & Evolutionary Biology
> U. of Tennessee, Knoxville
>