On Tue, Apr 5, 2011 at 5:19 AM, Laura Iacolina <liacolina@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.lazarus@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)