[adegenet-forum] Parallel computing?

[Federico Calboli]

On 31 Mar 2015, at 01:20, Karl Fetter <karl.fetter at gmail.com> wrote:
> 
> Hi Adegenet Users,
> 
> I'm going to be running a DAPC on a large data set soon of about 167K SNPs.

I hate to be contrararian, BUT you will have a lot of SNPs that are in strong linkage, i.e. they will provide *extactly* the same information, adding nothing to your analysis aside from computational burden.

I know I am not a referee of your future paper, and thus you need not to, but you might actually get something out of convincing me ausing so many SNPs is actually beter that pruning them to a subset that have a much lower linkage between them (say, select SNPs with a pairwise R^2 of.5 in a window of 50 SNPs, that you slide 5 SNPs at a time until you have pruned the whole genome.  PLINK can do this for you). 


Cheers

F



> I want to run these commands in parallel and I'm very unfamiliar with the process. A quick google search brings me to several dozen R packages for parallel computing and I'm wondering, what's the latest and greatest package out there?
> 
> Thanks in advance!
> 
> Karl Fetter 
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