R: estimating genotyping error rate

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R: estimating genotyping error rate

MeriamNF
Hello,
I have SNP data from genotyping.
I would like to estimate the error rate between replicated samples using R.
How can I proceed?

Thanks
Meriam

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Re: R: estimating genotyping error rate

Bert Gunter-2
"How can I proceed?"

-- By doing your own homework about appropriate methodology and software
instead of asking others to do it for you.

-- and by posting as necessary on the appropriate website, which is most
likely Bioconductor Help, not here.


Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Jan 17, 2019 at 9:03 AM N Meriam <[hidden email]> wrote:

> Hello,
> I have SNP data from genotyping.
> I would like to estimate the error rate between replicated samples using R.
> How can I proceed?
>
> Thanks
> Meriam
>
> ______________________________________________
> [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: R: estimating genotyping error rate

Jeff Newmiller
I would say that you may well be asking the wrong question in the right mailing list. Your discipline-specific jargon is impeding communication... you need to know what specific steps you want to take using R. A good reason to start your line of questioning on the Bioconductor forum is that there may already be packages that wrap up your tasks at the high level where you are currently thinking... or not. Which is all another way to say essentially what Bert said... except that you may find yourself back here soon with a question about R rather than "SNP data" if they regard this as too easy to need a package.

One fairly reliable way to know that your question is ready for this list is that you can get the ball rolling with a reproducible example written in R [1][2][3].

[1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

[2] http://adv-r.had.co.nz/Reproducibility.html

[3] https://cran.r-project.org/web/packages/reprex/index.html (read the vignette)


On January 17, 2019 9:34:59 AM PST, Bert Gunter <[hidden email]> wrote:

>"How can I proceed?"
>
>-- By doing your own homework about appropriate methodology and
>software
>instead of asking others to do it for you.
>
>-- and by posting as necessary on the appropriate website, which is
>most
>likely Bioconductor Help, not here.
>
>
>Bert Gunter
>
>"The trouble with having an open mind is that people keep coming along
>and
>sticking things into it."
>-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
>On Thu, Jan 17, 2019 at 9:03 AM N Meriam <[hidden email]> wrote:
>
>> Hello,
>> I have SNP data from genotyping.
>> I would like to estimate the error rate between replicated samples
>using R.
>> How can I proceed?
>>
>> Thanks
>> Meriam
>>
>> ______________________________________________
>> [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.

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[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.