Help manipulating 23andme data in R - reproducing relationship results

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Help manipulating 23andme data in R - reproducing relationship results

lyle0
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]]

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Re: Help manipulating 23andme data in R - reproducing relationship results

Jeff Newmiller
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:<[hidden email]>        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 <[hidden email]> 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]]
>
>______________________________________________
>[hidden email] 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.

______________________________________________
[hidden email] 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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Re: Help manipulating 23andme data in R - reproducing relationship results

Bert Gunter
(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
<[hidden email]> 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:<[hidden email]>        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 <[hidden email]> 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]]
>>
>>______________________________________________
>>[hidden email] 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.
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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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Re: Help manipulating 23andme data in R - reproducing relationship results

lyle0
Thanks Jeff, Bert!

You are right - definitely out of my skill area.. I've no found some help
on the bioconductor mailing list.

On 18 May 2015 at 03:04, Bert Gunter <[hidden email]> 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
> <[hidden email]> 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:<[hidden email]>        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 <[hidden email]> 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]]
> >>
> >>______________________________________________
> >>[hidden email] 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.
> >
> > ______________________________________________
> > [hidden email] 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]]

______________________________________________
[hidden email] 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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Re: Help manipulating 23andme data in R - reproducing relationship results

Martin Morgan-2
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 <[hidden email]> 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
>> <[hidden email]> 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:<[hidden email]>        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 <[hidden email]> 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]]
>>>>
>>>> ______________________________________________
>>>> [hidden email] 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.
>>>
>>> ______________________________________________
>>> [hidden email] 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]]
>
> ______________________________________________
> [hidden email] 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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Phone: (206) 667-2793

______________________________________________
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and provide commented, minimal, self-contained, reproducible code.