On Tue, Apr 5, 2011 at 5:19 AM, Laura Iacolina <liacol...@uniss.it> wrote:
> Considering I have to analyse 200 samples with 50K markers is there any way
to tell R to analyse each SNP one after the other?

From: Ross [mailto:ross.laza...@gmail.com]
> There are some Galaxy wrappers for plink
> (http://pngu.mgh.harvard.edu/~purcell/plink/) that may be useful for
> some kinds of analysis available in the rgenetics tools if you have
> linkage pedigree genotype and map files.

I would also advise using plink for this. Calculating SNP marker statistics
[1] is the one of the things that it has been designed to do. The main
problem is getting data into a format supported by plink, either linkage (one
line per individual), or transposed pedigree (one line per marker). There are
details on these formats in the plink documentation [2].

[1] http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#freq
[2] http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr

David Eccles (gringer)

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