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.silver...@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]]
______________________________________________
R-help@r-project.org mailing list
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.
______________________________________________
R-help@r-project.org mailing list
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.
______________________________________________
R-help@r-project.org mailing list
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.
