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Comparing 2 different files in R

7 messages · Rolf Turner, Lyle Warren, John Kane +1 more

Original
Lyle Warren
# 
Hi,

I have multiple files that I want to compare in R. They contain SNP data
with genotype in the 4th column, which is what I want to compare.

Is there any easy way to do this?
Rolf Turner
#
On 17/05/15 10:32, Lyle Warren wrote:
Yes.  Learn to use R.

cheers,

Rolf Turner
John Kane
# 
Probably but since you  have not told us anything about what you are doing it is difficult to say.  

You might find these links helpful http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and http://adv-r.had.co.nz/Reproducibility.html


John Kane
Kingston ON Canada
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Lyle Warren
# 
Thanks and sorry for being light on detail.

I have multiple files of raw human genome SNP data. Very large - the
compressed zip files are about 8mb large.
On 17 May 2015 at 20:53, John Kane <jrkrideau at inbox.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      John Kane
    

    

      
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John Kane
Kingston ON Canada

-----Original Message-----
From: lyle00 at gmail.com
Sent: Sun, 17 May 2015 20:56:24 +1000
To: jrkrideau at inbox.com
Subject: Re: [R] Comparing 2 different files in R
This is not an area I am going to be able to help with but we still need a lot more information I think.

At the moment we know nothing about the structure of the data, what you are trying to accomplish, in substantive terms, and what you may have tried.  As I say. I know nothing about the area but perhaps we need to know if all you want is to see if the SNP's are the same in different files, do you need summary stats or graphics. Come to think of it, something like a journal abstract might do nicely.

It may be that more knowlegeable people can recommend useful approaches or suggest that your type of analysis is more suitable in the Bioconductor lists.

Ideally we should see any 'minimal' code you may have written in R if any, &  some sample data is possible. See ?dput for a handy way to provide data but we,  hopefully, don't need to see 8mg of data. Probably just the first few lines of data would do.  A command like dput(head(50)) should be enough. See ?dput and?head for what these are doing or have a look at the links provided earlier.  For various reasons dput() is about the best method available for passing data to a help list or forum.  

Oh and one more thing. You seem to have sent this last post in HTML. The R-help list is plain-text so we would ask that you send everything in plain. HTML is stripped away and the resulting plain text can be so close to unintelligible that many readers will just ignore it.
==============================================
Thanks and sorry for being light on detail.?

I have multiple files of raw human genome SNP data. Very large - the compressed zip files are about 8mb large.?

        
On 17 May 2015 at 20:53, John Kane <jrkrideau at inbox.com> wrote:

        
Probably but since you? have not told us anything about what you are doing it is difficult to say.

 You might find these links helpful http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example [http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example] and http://adv-r.had.co.nz/Reproducibility.html [http://adv-r.had.co.nz/Reproducibility.html]

 John Kane
 Kingston ON Canada

 > -----Original Message-----
 > From: lyle00 at gmail.com
 > Sent: Sun, 17 May 2015 08:32:45 +1000
 > To: r-help at r-project.org
 > Subject: [R] Comparing 2 different files in R
 >
 > Hi,
 >
 > I have multiple files that I want to compare in R. They contain SNP data
 > with genotype in the 4th column, which is what I want to compare.
 >
 > Is there any easy way to do this?
 >

            

      
      
      
    

        
>
 > ______________________________________________
 > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
 > https://stat.ethz.ch/mailman/listinfo/r-help [https://stat.ethz.ch/mailman/listinfo/r-help]
 > PLEASE do read the posting guide
 > http://www.R-project.org/posting-guide.html [http://www.R-project.org/posting-guide.html]
 > and provide commented, minimal, self-contained, reproducible code.

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      Ben Tupper
    

    

      
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Hi,

        
On May 17, 2015, at 6:56 AM, Lyle Warren <lyle00 at gmail.com> wrote:

        

            

      
      
      
    

        
You'll have better luck asking on the Bioconductor help list ( http://www.bioconductor.org/ ) You may want to start here...

http://www.bioconductor.org/help/support/posting-guide/

and here...

http://www.bioconductor.org/help/search/index.html?q=SNP


Cheers,
Ben

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Lyle Warren
    

    

      
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Thanks Ben!

        
On 17 May 2015 at 23:14, Ben Tupper <ben.bighair at gmail.com> wrote: