[R] Re; Getting SNPS from PLINK to R

[Natalie Van Zuydam]

Hi Jim,

If you convert the ped and map files to binary plink files the .bim file 
will tell you the name and the position of the snps.  This would be the 
easiest method.  Alternatively packages like GenABEL and genetics have 
functions to read in PLINK formatted data for analysis in R.

Best wishes,
Natalie

On 21/06/2011 14:23, Clemontina Alexander wrote:
> Hi,
> If you go to this site:
> http://pngu.mgh.harvard.edu/~purcell/plink/res.shtml#teach
>
> And download the teaching.zip file, I think there was information in
> the word document about reading plink data into R, though I am not
> 100% sure. I think a read.table("filename.ped", header=T)  command may
> be enough. The word document is for plink beginners so it may not be
> what you are looking for.
>
> Tina
>
>
>
>
>
>
>
> On Mon, Jun 20, 2011 at 11:32 PM, Jim Silverton<jim.silverton at gmail.com>  wrote:
>> I a using plink on a large SNP dataset with a .map and .ped file.
>> I want to get some sort of file say a list of all the SNPs that plink is
>> saying that I have. ANyideas on how to do this?
>>
>> --
>> Thanks,
>> Jim.
>>
>>         [[alternative HTML version deleted]]
>>
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