useR! 2013 R / Bioconductor for Analysis and Comprehension of High-Throughput Genomic Data http://bioconductor.org/help/course-materials/2013/useR2013/Bioconductor-tutorial.pdf
It is not clear from your question which sort of help do you want in PLINK. I guess you are looking for tutorial on it ... Please check this http://www.vipbg.vcu.edu/~sarahme/eg/c16/practicals_C16.pdf for more detail.