I have some experience working with plink but R software is probably more versatile than plink... Did you find any disadventage working in R?
PLINK is better. right from splitting the large whole genome files to performing Quality control PLINK is better according to me.
PLINK needs a structured data (PED and MAP file or binary version of those). R can handle more complicated data. PLINK is easy to run, underlying code is C. R can be slow and sometimes needs a more powerful infrastructure. R is defiinitely more versatile, especially for meta-analysis, time to event etc.
I agree with Joseph, I tried plink to analyse some 'plink formatted' data but it failed because there was no .ped file. I went for R because it was more flexible to read arbitrary data sets, and more flexible in follow-on analyses and plotting options. You might prefer plink if you don't like programming, but then again it doesn't look like it would be a 'simple' option.
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