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R: estimating genotyping error rate

3 messages · N Meriam, Bert Gunter, Jeff Newmiller

N Meriam
# 
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
Bert Gunter
# 
"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 <meriam.nef at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
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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 <bgunter.4567 at gmail.com> wrote: