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  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 .  http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#freq  http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr -- David Eccles (gringer) ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/