[R] Help manipulating 23andme data in R - reproducing relationship results

Martin Morgan mtmorgan at fredhutch.org
Sun May 17 23:04:45 CEST 2015


On 05/17/2015 01:52 PM, Lyle Warren wrote:
> Thanks Jeff, Bert!
>
> You are right - definitely out of my skill area.. I've no found some help
> on the bioconductor mailing list.

I'm not sure that you've asked in the right place

   https://support.bioconductor.org

see also http://www.vincebuffalo.com/2012/03/12/23andme-gwascat.html which is a 
little dated and maybe not relevant to your question.

A little tangentially, see also https://support.bioconductor.org/p/67444/

Martin Morgan

>
> On 18 May 2015 at 03:04, Bert Gunter <gunter.berton at gene.com> wrote:
>
>> (No response necessary)
>>
>> What struck me about this post was the apparent mismatch: the OP
>> seemed not to have a clue where to begin. Maybe he somehow has been
>> assigned or chose a task for which his skills and background are
>> inadequate. This is not really a criticism: if someone told me to make
>> a dining room set, my reply would be: "Either find someone else or see
>> you in about a year after which I may have learned enough to attempt
>> the task. "
>>
>> So maybe the OP should give up looking for internet advice altogether
>> and find someone local to work with?
>>
>> And, of course, apologies if I have misinterpreted.
>>
>> Cheers,
>> Bert
>>
>>
>>
>> Bert Gunter
>> Genentech Nonclinical Biostatistics
>> (650) 467-7374
>>
>> "Data is not information. Information is not knowledge. And knowledge
>> is certainly not wisdom."
>> Clifford Stoll
>>
>>
>>
>>
>> On Sun, May 17, 2015 at 9:52 AM, Jeff Newmiller
>> <jdnewmil at dcn.davis.ca.us> wrote:
>>> This is a very domain-specific question (genetic data analysis), not so
>> much a question about how to use R, so does not seem on topic here. I also
>> suspect that the company 23andme may use some proprietary algorithms, so
>> "replicating their results" could be a tall order.
>>>
>>> You might start with the CRAN "Statistical Genetics" task view, and a
>> textbook on the subject. The Bioconductor project may also be a useful
>> resource.
>>>
>> ---------------------------------------------------------------------------
>>> Jeff Newmiller                        The     .....       .....  Go
>> Live...
>>> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live
>> Go...
>>>                                        Live:   OO#.. Dead: OO#..  Playing
>>> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
>>> /Software/Embedded Controllers)               .OO#.       .OO#.
>> rocks...1k
>>>
>> ---------------------------------------------------------------------------
>>> Sent from my phone. Please excuse my brevity.
>>>
>>> On May 16, 2015 6:53:46 AM PDT, Lyle Warren <lyle00 at gmail.com> wrote:
>>>> Hi,
>>>>
>>>> I'm trying to replicate 23andMe's parentage test results within R,
>>>> using
>>>> the 23andme raw data. Does anyone know a simple way to do this? I have
>>>> read
>>>> the data with gwascat and it seems to be in there fine.
>>>>
>>>> Thanks for any help you can give!
>>>>
>>>> Cheers,
>>>>
>>>> Lyle
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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